Kissplice2reftranscriptome error : IndexError

Question

[jfo]

Hello,

I am trying to run the last part of kissplice pipeline, which is kissplice2reftranscriptome and got this error:

command:

kissplice2reftranscriptome -b ORP_corset_all_longest.fasta.transdeco der.bed -k kissplice_out_Fask41_coherents_type_0a.fa -t out_blat_SNP_ORP_ID_80.psl -o mainOutput.tsv -l lowQueryCOverageOutput.tsv

error:

Opening all files and formatting tables...

Collecting data...

Traceback (most recent call last):

File "/home/user/src/anaconda2/bin/kissplice2reftranscriptome", line 4, in <module> __import__('pkg_resources').run_script('kissplice2reftranscriptomelib==1.3.2', 'kissplice2reftranscriptome')

File "/home/user/src/anaconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 748, in run_script self.require(requires)[0].run_script(script_name, ns)

File "/home/user/src/anaconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1524, in run_script exec(script_code, namespace, namespace)

File "/home/user/src/anaconda2/lib/python2.7/site-packages/kissplice2reftranscriptomelib-1.3.2-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 577, in <module> File "/home/usr/src/anaconda2/lib/python2.7/site-packages/kissplice2reftranscriptomelib-1.3.2-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 223, in main

File "build/bdist.linux-x86_64/egg/kissplice2reftranscriptomelib/dataAnalysis/blatBasicData.py", line 101, in getGeneTable

IndexError: list index out of range

Additional Information:

The only deviation of my analysis from the guide/documentation is that I did not use Trinity for de novo assembly.

Thank you.

Answer 1

[vincent.lacroix]

Dear user,

This bug should now be solved with version 1.3.3 of k2rt available here: http://kissplice.prabi.fr/tools/kiss2rt/ When using >30 input files to KisSplice, the fasta header gets very long, and blat truncates it when creating .psl files, which causes downstream issues in k2rt. This is now fixed.

Regarding the use of another transcriptome assembler than Trinity, I think it should run fine. We only use Trinity header for filling columns 11 and 12 (SNP_in_multiple_assembled_genes, SNP_in_multiple_assembled_isoforms): c1_g1_i1 and c1_g1_i2 are interpreted as two isoforms of the same gene, while c1_g1_i1 and c2_g1_i1 are interpreted as two different genes. When using an alternative assembler, we will likely not be able to make this distinction, and most likely only one of these two columns will be interpretable.

Best,

Vincent

[jfo]

Thank you Vincent! Everything went smoothly now. :)