Comments (10)
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@JLTrincado & @EduEyras, should I try running diffSplice using an earlier version of SUPPA?
Actually, this may be solved by simply using the latest code on the repo.
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Hi Daniel,
Could you send us some lines of the files you're using?
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Yes, I can @JLTrincado. Which files do you want parts/lines of? The .ioi, the .tpm, and the .psi files? How should I send that?
BTW, using the latest code on GH didn't fix it.
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The best would me if you send me lines from all your files. You can email me: [email protected]
Thanks for your interest
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The .psi files are empty, so the prior step had failed. I only noticed now when I was making file excerpts.
These are the commands I used to generate the PSI files for the 2 conditions:
python ~/miniconda3/pkgs/suppa-2.3-py36_1/bin/suppa.py \
psiPerIsoform \
-g ~/ref_genome_files/Mus_musculus.GRCm38.92.gtf \
-e NS_GMTcDay1_merged.tpm \
-o NS_GMTcDay1_transcript_PSI
python ~/miniconda3/pkgs/suppa-2.3-py36_1/bin/suppa.py \
psiPerIsoform \
-g ~/ref_genome_files/Mus_musculus.GRCm38.92.gtf \
-e NS_control_merged.tpm \
-o NS_control_transcript_PSI
I will send you excerpts of the .tpm and .ioi files
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Related Issues (20)
- Problems replicating TRA2 tutorial results HOT 3
- DiffSplice significant results have dpsi values of 0 HOT 5
- Encountering errors when trying to process large numbers of samples with SUPPA2 DiffSplice HOT 1
- Definition of Positive and Negative is inconsistent with Fig 3 for 'Right' Alternative Terminal Exon Events
- A problem occur in step 'psiPerEvent' HOT 13
- Wondering will SUPPA generate different results while using the same file? HOT 1
- ERROR:lib.tools:['Unexpected number of fields. 3 expected, 2 given'] HOT 3
- Why this regions were not regarded as RI ? HOT 2
- Something went wrong with detection of A5 and A3 HOT 6
- Regarding pvalues in diffSplice HOT 1
- generateEvents missies some Retained Intron (RI) events HOT 5
- PSI normalization HOT 4
- getting nothing in results simple identification of AS events HOT 5
- Can diffsplice deal with condition only has one sample(no replications) HOT 2
- SUPPA not working on quantification HOT 10
- psiPerIsoform resulting in empty .psi file HOT 2
- psiperEvent not working HOT 6
- Problems on multipleFieldSelection.py
- psiPerEvent problem HOT 1
- Calculate differential splicing events HOT 11
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