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Xinglab / rmats2sashimiplot

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Help with rmats2sashimiplot #119

Open Sahu-Mousumi opened 9 months ago

Sahu-Mousumi commented 9 months ago

Hi!

Below is my rmats command

rmats.py --b1 b1.txt --b2 b2.txt --gtf gencode.v44.annotation.gtf --novelSS --allow-clipping -t paired --libType fr-firststrand --readLength 76 --variable-read-length --nthread $SLURM_CPUS_PER_TASK --od rmats_res --tmp tmp_rmats_res

I found CD58 is statistically significant-

chr chr1 strand - exonStart_0base 116536096 exonEnd 116536228 upstreamES 116521905 upstreamEE 116521983 downstreamES 116544310 downstreamEE 116544604 ID.1 151386 IJC_SAMPLE_1 45,49,64,35 SJC_SAMPLE_1 0,2,0,0 IJC_SAMPLE_2 38,49,65,53,38,38 SJC_SAMPLE_2 1,6,0,3,0,5 IncFormLen 150 SkipFormLen 75 PValue 0.00028013 FDR 0.04768118

But while plotting shahimi using rMATS2Shashimiplot, I am generating below error-

File "/home/.local/lib/python3.10/site-packages/MISO/misopy/sashimi_plot/sashimi_plot.py", line 140

raise Exception, "Cannot find file %s. Are you sure the events " \

Should I use any filter or any suggestion??

Thanks Mousumi

EricKutschera commented 9 months ago

There are a couple other posts that had the Cannot find file error: https://github.com/Xinglab/rmats2sashimiplot/issues/61 https://github.com/Xinglab/rmats2sashimiplot/issues/62

In both of those cases there was an earlier error message that was the main issue. The particular issue in those other posts is fixed in v3.0.0

Can you post the full output from rmats2sashimiplot?