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error with diffSplice about suppa HOT 10 CLOSED

comprna avatar comprna commented on August 13, 2024
error with diffSplice

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EduEyras avatar EduEyras commented on August 13, 2024

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EduEyras avatar EduEyras commented on August 13, 2024

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danfulop avatar danfulop commented on August 13, 2024

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danfulop avatar danfulop commented on August 13, 2024

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danfulop avatar danfulop commented on August 13, 2024

@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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JLTrincado avatar JLTrincado commented on August 13, 2024

Hi Daniel,

Could you send us some lines of the files you're using?

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danfulop avatar danfulop commented on August 13, 2024

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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JLTrincado avatar JLTrincado commented on August 13, 2024

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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danfulop avatar danfulop commented on August 13, 2024

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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EduEyras avatar EduEyras commented on August 13, 2024

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