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Xinglab / PEGASAS

Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)
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Error in pathway part #1

Closed hust-yyan closed 3 years ago

hust-yyan commented 3 years ago

Hello, I was going to use Pegasas to annotate the rmats output functionally, and then I ran the following command: outdir=/home/PROJECTS/LungCancer/RNAseq/AS/rmats_secondrun/PEGASAS_output geneExpbySample=/data1/yyan_tmp/LUNG_CANCER/analysis/deseq2_output/all_genes_FPKM_symbol.txt geneSignatureList=/home/yyan/database/MSigDB/h.all.v7.2.symbols.gmt groupInfo=/data1/yyan_tmp/LUNG_CANCER/analysis/deseq2_output/grouping_info.txt PEGASAS pathway \ -o $outdir -n 2 --plotting \ $geneExpbySample $geneSignatureList $groupInfo I got the following error message: image this is the geneExpbySample file that I used: image Could you please help me to see what the problem is?

ypnngaa-py commented 3 years ago

Hello, The expression format looks ok(but you may have to remove '"' otherwise it will report another error). The error in the screenshot is about the format of geneSignatureList input. Can you double check the format of that file? And please check this https://github.com/Xinglab/PEGASAS#example-pegasas-run from the README, where we provided an example format of the signature input (can be found here: PEGASAS/data/hallmarks50-2.gmt.txt). It is slightly different than the ones directly downloaded MSigDB, for the purpose of analyzing multiple signatures.

Let me know. Yang

hust-yyan commented 3 years ago

Thank you very much, this problem is solved now.