Question: prepDE KeyError on MSTRG
0
gravatar for shintzen
6 months ago by
shintzen0
shintzen0 wrote:

I am trying to run prepDE (found here http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) however I am getting an error that does not give me a lot of information on what exactly the issue is or where to look on where to solve it. I googled but didn't find much. 

C:\Python27\python.exe prepDE.py -i C:\sample_lst.txt
0 1683-bulk
1 1680-bulk
Traceback (most recent call last):
  File "C:\prepDE.py", line 269, in <module>
    geneDict.setdefault(geneIDs[i], {})  # gene_id
KeyError: 'MSTRG.23895.4'

I tried printing the values to get a sense of the issue but it is taking a long time to complete. Has anyone seen this error, how did you resolve it? 

deseq2 prepde • 148 views
ADD COMMENTlink modified 6 months ago by Michael Love24k • written 6 months ago by shintzen0
1

KeyError means you're trying to use a key which doesn't exist. I think that might mean you have different transcripts in your sample gtf files. 

ADD REPLYlink modified 6 months ago • written 6 months ago by lefeverde10
Answer: prepDE KeyError on MSTRG
0
gravatar for Michael Love
6 months ago by
Michael Love24k
United States
Michael Love24k wrote:

I don’t maintain this software or script. You’ll have better luck with the maintainers.

ADD COMMENTlink written 6 months ago by Michael Love24k
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