Comments (10)
@WYSNI Happy to see your interest in RNACocktail. Would you please let me know what version of bedtools and pybedtools you are using?
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I'm using pybedtools 0.7.7 and bedtools 2.26.0 on a conda environment. Is it a bedtools version problem in your opinion?
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@WYSNI I recall bedtools 2.26.0 had some issues with groupby
. Would you please use later versions of bedtools like 2.27 ?
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It's works! Thanks a lot
I don't understand why GIREMI return a 1 code in steps 6 and 9 despite I have giremi_out.txt.res and it seems good
giremi_out.txt.res
Any idea?
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@WYSNI the first return code of 1 is normal, as we do it in two iterations. For the second one you can check the giremi.log
file at work/giremi/A
for more specific logs. In my experience as long as giremi_out.txt.res
exists and has the ifRNA
column the predictions should be OK. You can also check whether giremi_out.txt.res
covers all your region. Also, check how many 1
's you have in the if RNA
(last) column.
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Ok Thanks! I have some "1" in my ifRNAE column so I think the result is ok.
Last question: can I used files on the test directory ( GRCh37_genes_pos.bed.gz, GRCh37_strand_pos.bed.gz, GRCh38_genes_pos.bed.gz, GRCh38_strand_pos.bed.gz) for my experiments or are they not complete ?
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@WYSNI Yes they are complete for whole genome GRCh37 and GRCh38 references.
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Thanks a lot!
I close this issue.
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Hi,
Sorry, I reopen this issue because I have another problem with the step 5 of the editing mode...
I think the problem is again in line 88 of the editing.py file but with the groupby now.
I'm on a conda environment with bedtools 2.27.1 and pybedtools 0.7.7.
My environment (RNACocktail) path is in the first place of my $PATH:
I don't understand what's going on!
Any suggestion?
Thanks, WYSNI
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Ok my bad, it's just a problem of chromosome name on GRCh38 files of the test/ repository.
Sorry!
I (re)closed this issue.
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Related Issues (12)
- Variant Calling HOT 2
- GIREMI failed! HOT 10
- Error in run_editing STEP 10 HOT 3
- Keep moving HOT 4
- docker test fails on fusioncatcher in 0.3.0 HOT 1
- Transcript quantification of pacbio long reads (ccs)
- option '-k' is only recognised by salmon quant of salmon version 0.11.0 but not above
- samtools version 1.3 or higher incompatible HOT 1
- IOError: [Errno 36] File name too long: HOT 2
- hisat2_jun2bed.py error HOT 1
- Cannot start run_rnacocktail.py HOT 3
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