KisSplice2refgenome error message

Question

[sophie.paillard]

Dear all,

I'm trying to run kisSplice2refgenome with the following command line :

kissplice2refgenome -a annotation_file.gtf  output_starlong.sam --pairedEnd True --counts 2 --exonicReads False --readLength 101 --overlap 54

annotation_file.gtf is our annotation file, output_starlong.sam is the output we obtained running STARLONG on the output file (type1.fa, AS file) from kisSplice and STAR-index, and our read length is 101.

I get this error message :

File "/kissplice2refgenome-1.0.1/kissplice2refgenomelib/events.py", line 94, in PSIcalc
    for k in range(len(countsUpValues)) :
UnboundLocalError: local variable 'countsUpValues' referenced before assignment

Did anybody already get this error message and could you please help me to fix the problem ? Thanks in advance !

Answer 1

[vincent.lacroix]

Dear Sophie,

I think the best solution is to use k2rg without any option.

kissplice2refgenome -a annotation_file.gtf  output_starlong.sam

This should work fine. The other options are used to have a good estimation of the Percent Spliced In (PSI). If you do not use them, the output file should be correct. Only the PSI column will be affected. But you can simply disregard this column, or consider it as suboptimal estimations.

In practice, we rarely use the PSI estimations given by k2rg. We mostly use the PSI estimations given by KissDE, which is the next step in the pipeline we present here: http://kissplice.prabi.fr/pipeline_ks_farline/

But thanks for reporting this bug, we will look into it, and fix it for the next k2rg release. Don't hesitate if you have any more questions,

Best,

Vincent