A problem occur in step 'psiPerEvent'

[Tomcxf]

A problem occur in step 'psiPerEvent'

[EduEyras]

Hi, thanks for your email if there is no expression data, or the transcripts in the denominator of the PSI formula have zero expression, the PSI output will be NA for those events. It will also produce an NA if you're using a threshold for the total expression of the transcripts involved in the event (-f parameter) The cases that you get with NA should fall into either of these possibilities Please let me know if this is not the case cheers Eduardo

…

On Fri, 1 Jul 2022 at 12:44, Tomcxf ***@***.***> wrote: Hi developer！ Glad to meet such a convenience tool for AS! I have a probem in psiPerEvent: When I type suppa.py psiPerEvent It shows that ERROR:psiCalculator:transcript rna-XM_025824875.2 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event gene-LOC112782481;SE:NC_037637.1:143909122-143910558:143910623-143911863:+. INFO:lib.tools:File ../Ti1_events.ioe closed. INFO:psiCalculator:Generating output Ti1_events.psi INFO:psiCalculator:Done I know that it means some transcript is not expressed in some condition ,and it is common. But when I check the output file ,the second line value are all "NA". I also grep the "not found" transcript name from count.txt, it shows that some of them are located in count.txt. So I don't know how to do. Hope you can help me ,tks! The gtf files: 1 NC_037618.1 Gnomon transcript 19151 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC1 2 NC_037618.1 Gnomon exon 19151 19514 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 3 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 4 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 5 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 6 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 7 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 8 NC_037618.1 Gnomon exon 24512 24550 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 9 NC_037618.1 Gnomon exon 25238 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 10 NC_037618.1 Gnomon CDS 20456 20598 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 11 NC_037618.1 Gnomon CDS 21087 21163 . + 1 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 12 NC_037618.1 Gnomon CDS 21687 21790 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 13 NC_037618.1 Gnomon CDS 22333 22513 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 14 NC_037618.1 Gnomon CDS 23069 23358 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 15 NC_037618.1 Gnomon CDS 24512 24550 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 16 NC_037618.1 Gnomon CDS 25238 25531 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 17 NC_037618.1 Gnomon transcript 19152 25346 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC1 18 NC_037618.1 Gnomon exon 19152 19514 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 19 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 20 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 21 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 22 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 23 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 24 NC_037618.1 Gnomon exon 24235 24420 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 the count.txt 1 Ti1 2 XM_025811832.1 19755.401789589017 3 XM_025765549.2 9328.354692260724 4 XM_025818714.2 8906.955351091321 5 XM_025756615.2 7793.086122439508 6 XM_025790760.2 5414.81358060074 7 XM_025755464.1 4826.56026077942 8 XM_025765548.1 4364.468766061501 9 XM_025839483.1 4180.543656598884 10 XM_025791944.1 4060.072984999109 11 XM_025838818.1 3838.3220091481867 12 XM_025809869.2 3584.5834452211607 13 XM_025796094.1 3369.9574032027676 14 XM_025800780.2 3183.77330657713 15 XM_025765562.2 3113.0008093724455 — Reply to this email directly, view it on GitHub <#147>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

[Tomcxf]

Hi, thanks for your email if there is no expression data, or the transcripts in the denominator of the PSI formula have zero expression, the PSI output will be NA for those events. It will also produce an NA if you're using a threshold for the total expression of the transcripts involved in the event (-f parameter) The cases that you get with NA should fall into either of these possibilities Please let me know if this is not the case cheers Eduardo
…
On Fri, 1 Jul 2022 at 12:44, Tomcxf @.> wrote: Hi developer！ Glad to meet such a convenience tool for AS! I have a probem in psiPerEvent: When I type suppa.py psiPerEvent It shows that ERROR:psiCalculator:transcript rna-XM_025824875.2 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event gene-LOC112782481;SE:NC_037637.1:143909122-143910558:143910623-143911863:+. INFO:lib.tools:File ../Ti1_events.ioe closed. INFO:psiCalculator:Generating output Ti1_events.psi INFO:psiCalculator:Done I know that it means some transcript is not expressed in some condition ,and it is common. But when I check the output file ,the second line value are all "NA". I also grep the "not found" transcript name from count.txt, it shows that some of them are located in count.txt. So I don't know how to do. Hope you can help me ,tks! The gtf files: 1 NC_037618.1 Gnomon transcript 19151 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC1 2 NC_037618.1 Gnomon exon 19151 19514 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 3 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 4 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 5 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 6 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 7 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 8 NC_037618.1 Gnomon exon 24512 24550 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 9 NC_037618.1 Gnomon exon 25238 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 10 NC_037618.1 Gnomon CDS 20456 20598 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 11 NC_037618.1 Gnomon CDS 21087 21163 . + 1 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 12 NC_037618.1 Gnomon CDS 21687 21790 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 13 NC_037618.1 Gnomon CDS 22333 22513 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 14 NC_037618.1 Gnomon CDS 23069 23358 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 15 NC_037618.1 Gnomon CDS 24512 24550 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 16 NC_037618.1 Gnomon CDS 25238 25531 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 17 NC_037618.1 Gnomon transcript 19152 25346 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC1 18 NC_037618.1 Gnomon exon 19152 19514 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 19 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 20 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 21 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 22 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 23 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 24 NC_037618.1 Gnomon exon 24235 24420 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 the count.txt 1 Ti1 2 XM_025811832.1 19755.401789589017 3 XM_025765549.2 9328.354692260724 4 XM_025818714.2 8906.955351091321 5 XM_025756615.2 7793.086122439508 6 XM_025790760.2 5414.81358060074 7 XM_025755464.1 4826.56026077942 8 XM_025765548.1 4364.468766061501 9 XM_025839483.1 4180.543656598884 10 XM_025791944.1 4060.072984999109 11 XM_025838818.1 3838.3220091481867 12 XM_025809869.2 3584.5834452211607 13 XM_025796094.1 3369.9574032027676 14 XM_025800780.2 3183.77330657713 15 XM_025765562.2 3113.0008093724455 — Reply to this email directly, view it on GitHub <#147>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA . You are receiving this because you are subscribed to this thread.Message ID: @.>
-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

I don't know if expression data can general zero expression. Because I grep some transcript "not found" in expression file as the error mentioned ,I found their tpm are not zero in expression file.
For example:

ERROR:psiCalculator:transcript rna-XM_025826174.1 not found in the "expression file".
ERROR:psiCalculator:PSI not calculated for event gene-LOC112783286;AL:NC_037637.1:141037510
141038041:141038247:141037510-141038365:141039007:+.

when i type grep rna-XM_025826174.1 transcript_counts.txt

It shows
rna-XM_025826174.1 0.9754517804921867

And I think it's weird that all the transcript are zero.

By the way, I don't know the threshold you mentioned is a option in SUPPA or some other software which can QC.
Thanks!

[EduEyras]

Hi, yes, it is the "-f" option in the psiPerEvent command I am wondering if python has a problem managing an ID with "-" on it? Does this happen to transcript IDs without "-" on them? What's the entry in the .ioe file for the event where this transcript occurs? cheers Eduardo

…

On Fri, 1 Jul 2022 at 13:14, Tomcxf ***@***.***> wrote: Hi, thanks for your email if there is no expression data, or the transcripts in the denominator of the PSI formula have zero expression, the PSI output will be NA for those events. It will also produce an NA if you're using a threshold for the total expression of the transcripts involved in the event (-f parameter) The cases that you get with NA should fall into either of these possibilities Please let me know if this is not the case cheers Eduardo … <#m_-3062299682085211119_> On Fri, 1 Jul 2022 at 12:44, Tomcxf *@*.*> wrote: Hi developer！ Glad to meet such a convenience tool for AS! I have a probem in psiPerEvent: When I type suppa.py psiPerEvent It shows that ERROR:psiCalculator:transcript rna-XM_025824875.2 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event gene-LOC112782481;SE:NC_037637.1:143909122-143910558:143910623-143911863:+. INFO:lib.tools:File ../Ti1_events.ioe closed. INFO:psiCalculator:Generating output Ti1_events.psi INFO:psiCalculator:Done I know that it means some transcript is not expressed in some condition ,and it is common. But when I check the output file ,the second line value are all "NA". I also grep the "not found" transcript name from count.txt, it shows that some of them are located in count.txt. So I don't know how to do. Hope you can help me ,tks! The gtf files: 1 NC_037618.1 Gnomon transcript 19151 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC1 2 NC_037618.1 Gnomon exon 19151 19514 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 3 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 4 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 5 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 6 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 7 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 8 NC_037618.1 Gnomon exon 24512 24550 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 9 NC_037618.1 Gnomon exon 25238 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 10 NC_037618.1 Gnomon CDS 20456 20598 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 11 NC_037618.1 Gnomon CDS 21087 21163 . + 1 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 12 NC_037618.1 Gnomon CDS 21687 21790 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 13 NC_037618.1 Gnomon CDS 22333 22513 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 14 NC_037618.1 Gnomon CDS 23069 23358 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 15 NC_037618.1 Gnomon CDS 24512 24550 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 16 NC_037618.1 Gnomon CDS 25238 25531 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 17 NC_037618.1 Gnomon transcript 19152 25346 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC1 18 NC_037618.1 Gnomon exon 19152 19514 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 19 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 20 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 21 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 22 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 23 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 24 NC_037618.1 Gnomon exon 24235 24420 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 the count.txt 1 Ti1 2 XM_025811832.1 19755.401789589017 3 XM_025765549.2 9328.354692260724 4 XM_025818714.2 8906.955351091321 5 XM_025756615.2 7793.086122439508 6 XM_025790760.2 5414.81358060074 7 XM_025755464.1 4826.56026077942 8 XM_025765548.1 4364.468766061501 9 XM_025839483.1 4180.543656598884 10 XM_025791944.1 4060.072984999109 11 XM_025838818.1 3838.3220091481867 12 XM_025809869.2 3584.5834452211607 13 XM_025796094.1 3369.9574032027676 14 XM_025800780.2 3183.77330657713 15 XM_025765562.2 3113.0008093724455 — Reply to this email directly, view it on GitHub <#147 <#147>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA <https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA> . You are receiving this because you are subscribed to this thread.Message ID: @.*> -- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ I don't know if expression data can general zero expression. Because I grep some transcript "not found" in expression file as the error mentioned ,I found their tpm are not zero in expression file. For example: ERROR:psiCalculator:transcript rna-XM_025826174.1 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event gene-LOC112783286;AL:NC_037637.1:141037510 141038041:141038247:141037510-141038365:141039007:+. when i type grep rna-XM_025826174.1 transcript_counts.txt It shows rna-XM_025826174.1 0.9754517804921867 And I think it's weird that all the transcript are zero. By the way, I don't know the threshold you mentioned is a option in SUPPA or some other software which can QC. Thanks! — Reply to this email directly, view it on GitHub <#147 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB6PIJ6NH4L5S4HXCYDVRZPAPANCNFSM52LIKZQA> . You are receiving this because you commented.Message ID: ***@***.***>

[Tomcxf]

Hi, yes, it is the "-f" option in the psiPerEvent command I am wondering if python has a problem managing an ID with "-" on it? Does this happen to transcript IDs without "-" on them? What's the entry in the .ioe file for the event where this transcript occurs? cheers Eduardo
…
On Fri, 1 Jul 2022 at 13:14, Tomcxf @.> wrote: Hi, thanks for your email if there is no expression data, or the transcripts in the denominator of the PSI formula have zero expression, the PSI output will be NA for those events. It will also produce an NA if you're using a threshold for the total expression of the transcripts involved in the event (-f parameter) The cases that you get with NA should fall into either of these possibilities Please let me know if this is not the case cheers Eduardo … <#m_-3062299682085211119_> On Fri, 1 Jul 2022 at 12:44, Tomcxf @.> wrote: Hi developer！ Glad to meet such a convenience tool for AS! I have a probem in psiPerEvent: When I type suppa.py psiPerEvent It shows that ERROR:psiCalculator:transcript rna-XM_025824875.2 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event gene-LOC112782481;SE:NC_037637.1:143909122-143910558:143910623-143911863:+. INFO:lib.tools:File ../Ti1_events.ioe closed. INFO:psiCalculator:Generating output Ti1_events.psi INFO:psiCalculator:Done I know that it means some transcript is not expressed in some condition ,and it is common. But when I check the output file ,the second line value are all "NA". I also grep the "not found" transcript name from count.txt, it shows that some of them are located in count.txt. So I don't know how to do. Hope you can help me ,tks! The gtf files: 1 NC_037618.1 Gnomon transcript 19151 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC1 2 NC_037618.1 Gnomon exon 19151 19514 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 3 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 4 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 5 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 6 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 7 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 8 NC_037618.1 Gnomon exon 24512 24550 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 9 NC_037618.1 Gnomon exon 25238 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 10 NC_037618.1 Gnomon CDS 20456 20598 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 11 NC_037618.1 Gnomon CDS 21087 21163 . + 1 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 12 NC_037618.1 Gnomon CDS 21687 21790 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 13 NC_037618.1 Gnomon CDS 22333 22513 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 14 NC_037618.1 Gnomon CDS 23069 23358 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 15 NC_037618.1 Gnomon CDS 24512 24550 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 16 NC_037618.1 Gnomon CDS 25238 25531 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 17 NC_037618.1 Gnomon transcript 19152 25346 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC1 18 NC_037618.1 Gnomon exon 19152 19514 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 19 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 20 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 21 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 22 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 23 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 24 NC_037618.1 Gnomon exon 24235 24420 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 the count.txt 1 Ti1 2 XM_025811832.1 19755.401789589017 3 XM_025765549.2 9328.354692260724 4 XM_025818714.2 8906.955351091321 5 XM_025756615.2 7793.086122439508 6 XM_025790760.2 5414.81358060074 7 XM_025755464.1 4826.56026077942 8 XM_025765548.1 4364.468766061501 9 XM_025839483.1 4180.543656598884 10 XM_025791944.1 4060.072984999109 11 XM_025838818.1 3838.3220091481867 12 XM_025809869.2 3584.5834452211607 13 XM_025796094.1 3369.9574032027676 14 XM_025800780.2 3183.77330657713 15 XM_025765562.2 3113.0008093724455 — Reply to this email directly, view it on GitHub <#147 <#147>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA . You are receiving this because you are subscribed to this thread.Message ID: @.> -- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ I don't know if expression data can general zero expression. Because I grep some transcript "not found" in expression file as the error mentioned ,I found their tpm are not zero in expression file. For example: ERROR:psiCalculator:transcript rna-XM_025826174.1 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event gene-LOC112783286;AL:NC_037637.1:141037510 141038041:141038247:141037510-141038365:141039007:+. when i type grep rna-XM_025826174.1 transcript_counts.txt It shows rna-XM_025826174.1 0.9754517804921867 And I think it's weird that all the transcript are zero. By the way, I don't know the threshold you mentioned is a option in SUPPA or some other software which can QC. Thanks! — Reply to this email directly, view it on GitHub <#147 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB6PIJ6NH4L5S4HXCYDVRZPAPANCNFSM52LIKZQA . You are receiving this because you commented.Message ID: @.**>

OK, I try to delete "-" in transcript IDs and I get the same error. May be it doesn't work.

Take the rna-XM_025826174.1 as an example. I grep it from the .ioe file:

NC_037637.1 gene-LOC112783286 gene-LOC112783286;A3:NC_037637.1:141035988-141036087:141035988-141036093:+ rna-XM_025826174.1,rna-XM_025826175.1,rna-XM_025826170.2,rna-XM_025826166.2,rna-XM_025826169.2,rna-XM_025826171.2,rna-XM_025826172.2,rna-XM_029296331.1 rna-XM_029296331.1,rna-XM_025826170.2,rna-XM_025826175.1,rna-XM_025826169.2,rna-XM_025826168.2,rna-XM_025826171.2,rna-XM_025826172.2,rna-XM_025826174.1,rna-XM_025826166.2

By the way, I get the transcript_count.file from nanocount and it orginally don't have "rna-" in first line. I don't know whether it impede the process. When I use this file, it gets the same error.

[EduEyras]

The transcript IDs from the .ioe file and from the expression file have to match exactly. It looks like they're the same, so I don't understand why it does not work for some. unless there are some hidden characters added in the process of modifying the IDs? Having the right headers is also important, but that would give a general error, rather than an error for some transcripts only. If you send me the expression file for the transcripts for that event I can give it a try E.

…

On Fri, 1 Jul 2022 at 18:17, Tomcxf ***@***.***> wrote: Hi, yes, it is the "-f" option in the psiPerEvent command I am wondering if python has a problem managing an ID with "-" on it? Does this happen to transcript IDs without "-" on them? What's the entry in the .ioe file for the event where this transcript occurs? cheers Eduardo … <#m_-6266600544374418397_> On Fri, 1 Jul 2022 at 13:14, Tomcxf *@*.*> wrote: Hi, thanks for your email if there is no expression data, or the transcripts in the denominator of the PSI formula have zero expression, the PSI output will be NA for those events. It will also produce an NA if you're using a threshold for the total expression of the transcripts involved in the event (-f parameter) The cases that you get with NA should fall into either of these possibilities Please let me know if this is not the case cheers Eduardo … <#m_-3062299682085211119_> On Fri, 1 Jul 2022 at 12:44, Tomcxf @.> wrote: Hi developer！ Glad to meet such a convenience tool for AS! I have a probem in psiPerEvent: When I type suppa.py psiPerEvent It shows that ERROR:psiCalculator:transcript rna-XM_025824875.2 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event gene-LOC112782481;SE:NC_037637.1:143909122-143910558:143910623-143911863:+. INFO:lib.tools:File ../Ti1_events.ioe closed. INFO:psiCalculator:Generating output Ti1_events.psi INFO:psiCalculator:Done I know that it means some transcript is not expressed in some condition ,and it is common. But when I check the output file ,the second line value are all "NA". I also grep the "not found" transcript name from count.txt, it shows that some of them are located in count.txt. So I don't know how to do. Hope you can help me ,tks! The gtf files: 1 NC_037618.1 Gnomon transcript 19151 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC1 2 NC_037618.1 Gnomon exon 19151 19514 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 3 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 4 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 5 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 6 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 7 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 8 NC_037618.1 Gnomon exon 24512 24550 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 9 NC_037618.1 Gnomon exon 25238 25669 . + . transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 10 NC_037618.1 Gnomon CDS 20456 20598 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 11 NC_037618.1 Gnomon CDS 21087 21163 . + 1 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 12 NC_037618.1 Gnomon CDS 21687 21790 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 13 NC_037618.1 Gnomon CDS 22333 22513 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 14 NC_037618.1 Gnomon CDS 23069 23358 . + 2 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 15 NC_037618.1 Gnomon CDS 24512 24550 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 16 NC_037618.1 Gnomon CDS 25238 25531 . + 0 transcript_id "rna-XM_025826101.2"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 17 NC_037618.1 Gnomon transcript 19152 25346 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC1 18 NC_037618.1 Gnomon exon 19152 19514 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 19 NC_037618.1 Gnomon exon 20456 20598 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 20 NC_037618.1 Gnomon exon 21087 21163 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 21 NC_037618.1 Gnomon exon 21687 21790 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 22 NC_037618.1 Gnomon exon 22333 22513 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 23 NC_037618.1 Gnomon exon 23069 23358 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 24 NC_037618.1 Gnomon exon 24235 24420 . + . transcript_id "rna-XM_029293147.1"; gene_id "gene-LOC112783183"; gene_name "LOC112783183 the count.txt 1 Ti1 2 XM_025811832.1 19755.401789589017 3 XM_025765549.2 9328.354692260724 4 XM_025818714.2 8906.955351091321 5 XM_025756615.2 7793.086122439508 6 XM_025790760.2 5414.81358060074 7 XM_025755464.1 4826.56026077942 8 XM_025765548.1 4364.468766061501 9 XM_025839483.1 4180.543656598884 10 XM_025791944.1 4060.072984999109 11 XM_025838818.1 3838.3220091481867 12 XM_025809869.2 3584.5834452211607 13 XM_025796094.1 3369.9574032027676 14 XM_025800780.2 3183.77330657713 15 XM_025765562.2 3113.0008093724455 — Reply to this email directly, view it on GitHub <#147 <#147> <#147 <#147>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA <https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA> https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA <https://github.com/notifications/unsubscribe-auth/ADCZKB7DE5LHX76LTHG6NZ3VRZLPHANCNFSM52LIKZQA> . You are receiving this because you are subscribed to this thread.Message ID: @.> -- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna <https://github.com/comprna> http://scholar.google.com/citations?user=LiojlGoAAAAJ <http://scholar.google.com/citations?user=LiojlGoAAAAJ> I don't know if expression data can general zero expression. Because I grep some transcript "not found" in expression file as the error mentioned ,I found their tpm are not zero in expression file. For example: ERROR:psiCalculator:transcript rna-XM_025826174.1 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event gene-LOC112783286;AL:NC_037637.1:141037510 141038041:141038247:141037510-141038365:141039007:+. when i type grep rna-XM_025826174.1 transcript_counts.txt It shows rna-XM_025826174.1 0.9754517804921867 And I think it's weird that all the transcript are zero. By the way, I don't know the threshold you mentioned is a option in SUPPA or some other software which can QC. Thanks! — Reply to this email directly, view it on GitHub <#147 (comment) <#147 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB6PIJ6NH4L5S4HXCYDVRZPAPANCNFSM52LIKZQA <https://github.com/notifications/unsubscribe-auth/ADCZKB6PIJ6NH4L5S4HXCYDVRZPAPANCNFSM52LIKZQA> . You are receiving this because you commented.Message ID: @.***> OK, I try to delete "-" in transcript IDs and I get the same error. May be it doesn't work. Take the rna-XM_025826174.1 as an example. I grep it from the .ioe file: NC_037637.1 gene-LOC112783286 gene-LOC112783286;A3:NC_037637.1:141035988-141036087:141035988-141036093:+ rna-XM_025826174.1,rna-XM_025826175.1,rna-XM_025826170.2,rna-XM_025826166.2,rna-XM_025826169.2,rna-XM_025826171.2,rna-XM_025826172.2,rna-XM_029296331.1 rna-XM_029296331.1,rna-XM_025826170.2,rna-XM_025826175.1,rna-XM_025826169.2,rna-XM_025826168.2,rna-XM_025826171.2,rna-XM_025826172.2,rna-XM_025826174.1,rna-XM_025826166.2 By the way, I get the transcript_count.file from nanocount and it orginally don't have "rna-" in first line. I don't know whether it impede the process. When I use this file, it gets the same error. — Reply to this email directly, view it on GitHub <#147 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB5FX4QEELBQPAY5AHDVR2SQVANCNFSM52LIKZQA> . You are receiving this because you commented.Message ID: ***@***.***>

[Tomcxf]

Recently I did the same command again. Amazingly it works well. But now I still didn't figure out what happen. Anyway, thank you for taking so much time to solve my question! Thank you!

[Tomcxf]

By the way, I want to ask if SUPPA has visualization tools?
Or which plots can I use to show the result, Tks!

[EduEyras]

Hi, please have a look at the SUPPA tutorial in the wiki page https://github.com/comprna/SUPPA/wiki/SUPPA2-tutorial It has some suggestions to visualise the data with the corresponding code. I hope it helps E.

…

On Tue, 5 Jul 2022 at 16:05, Tomcxf ***@***.***> wrote: By the way, I want to ask if SUPPA has visualization tools? Or which plots can I use to show the result, Tks! — Reply to this email directly, view it on GitHub <#147 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKBZ5HJSI2M4EVQM5DWDVSPGEBANCNFSM52LIKZQA> . You are receiving this because you commented.Message ID: ***@***.***>

[Tomcxf]

Thank you !
My project has two condition without replicate. So is it common that in "Differential splicing analysis for transcripts and local events", it doesn't generate dpsi. file?
In suppa.py generateEvents step for local event, it doesn't generate GTF file. Is it because no replicate?
I search the issue of SUPPA. In an answer, you mentioned deltaPSI. I just wonder how can I get or count? Because I found it appear in dpsi. file but I didn't have.
Thank you!

[EduEyras]

Hi, The GTF of the events should be generated, because this is done by the generateEvents operation With no replicates you cannot use the DiffSplice operation, but there may be other things to identify potential candidates, One option is considering the deltaPSI as a function of the average expression level, and estimate a reasonable cutoff that is a function of the expression level. There are also methods like rMATs or MAJIQ that will do a test with the read counts, so you can use one single replicate per condition. I hope this helps E.

…

On Wed, 6 Jul 2022 at 20:09, Tomcxf ***@***.***> wrote: Thank you ! My project has two condition without replicate. So is it common that in "Differential splicing analysis for transcripts and local events", it doesn't generate dpsi. file? In suppa.py generateEvents step for local event, it doesn't generate GTF file. Is it because no replicate? I search the issue of SUPPA. In an answer, you mentioned deltaPSI. I just wonder how can I get or count? Because I found it appear in dpsi. file but I didn't have. Thank you! — Reply to this email directly, view it on GitHub <#147 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB66OUEUT5SHQVOUEHLVSVLNTANCNFSM52LIKZQA> . You are receiving this because you commented.Message ID: ***@***.***>

[Tomcxf]

Thank you for your help!

[Oliverfeudj]

Hello
I fell into the same error @EduEyras @Tomcxf have you please found any solution to this?
Thank you

[zjanna]

Dear Eduardo,
I have a problem using Suppa2 because at the end I get matrices with NA and messages: ERROR:psiCalculator:PSI not calculated for event...
for SALMON mapping I use the Homo_sapiens.GRCh38.cdna.all.fa.gz file, while in the SUPPA program to generateEvents I use Homo_sapiens.GRCh38.109.gtf....Could you suggest which fasta file and which gtf file to use here to get the transcripts count matrix?
Best regards, Joanna