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prepDE.py error - line 255 - gene ID related

Hi all,

I have been using the script provided by StringTie named 'prepDE.py' for getting gene and transcript abundances. It was working fine with another set of mouse samples but failing now with these set of human samples.

/Softwares/prepDE.py -i grouping-info.txt
0 Sample1
1 Sample2
Traceback (most recent call last):
  File "/Softwares/prepDE.py", line 255, in <module>
    geneDict.setdefault(geneIDs[i],{}) #gene_id
KeyError: 'Sample2.101064.1'

It seems there is some issue with the Gene ID - 101064.1. I checked for this name in the gtf files, but only 101064 is found. I tried removing a few samples as well but still it fails after the first sample run.

Please help if anyone has seen such an issue. I am using python version 3.5.

Thank you, Rituriya.

stringtie prepde.py geneid error rna-seq
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updated by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup • written by Rituriya • Rituriya

Hello Rituriya!

We believe that this post does not fit the main topic of this site.

Figured an issue on my end while processing the raw data. I had not given the right path in the grouping file! Wish the error said that rather than the one mentioned above.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Rituriya • Rituriya

1 answer

I would suggest useing R instead. There you can use tximport (from the tximport package) or IsoformSwitchAnalyzeR's importIsoformExpression() + isoformToGeneExp() - the later directly supports using the GTF file to get the isoform-to-gene mapping.

• 0 views • link
written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

Thank you Kristoffer for the details. I will give it a try.

• 0 views • link
written by Rituriya • Rituriya

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