error while Kissplice run

Question

[KG]

I am using kissplice to identify SNPs from the transcriptome data. I am getting an error. This is how my terminal looks like:

kissplice2refgenome -o Ct_SNP --pairedEnd PAIREDEND --vcf /home/mml/KG/Ct_STAR1.sam Run starts... Processing mapping information... Traceback (most recent call last): File "/usr/local/bin/kissplice2refgenome", line 4, in <module> __import__('pkg_resources').run_script('kissplice2refgenome==1.2.0', 'kissplice2refgenome') File "/home/mml/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/mml/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1534, in run_script exec(script_code, namespace, namespace) File "/usr/local/lib/python2.7/dist-packages/kissplice2refgenome-1.2.0-py2.7.egg/EGG-INFO/scripts/kissplice2refgenome", line 201, in <module>

File "/usr/local/lib/python2.7/dist-packages/kissplice2refgenome-1.2.0-py2.7.egg/EGG-INFO/scripts/kissplice2refgenome", line 166, in main

File "build/bdist.linux-x86_64/egg/kissplice2refgenomelib/fileLine.py", line 284, in getMappedEvents File "build/bdist.linux-x86_64/egg/kissplice2refgenomelib/fileLine.py", line 64, in setLine File "build/bdist.linux-x86_64/egg/kissplice2refgenomelib/fileLine.py", line 216, in getInfoKissplice File "build/bdist.linux-x86_64/egg/kissplice2refgenomelib/fileLine.py", line 43, in getInfoKissplice IndexError: list index out of range

Any help is appreciated.

Answer 1

[leandro.ishi.lima]

Dear KG,

I am redirecting your doubt to the other maintainers, but could you give us more details on the pipeline you are using to call SNPs from transcriptome data, if possible with the command lines?

We also propose the following pipeline: http://kissplice.prabi.fr/TWAS/ for SNP calling from RNA-seq data without a reference genome. I am not sure if you followed it, or if it is applicable to your dataset, or if you are trying another pipeline.

Thanks for the report.

Kind regards.

Answer 2

[KG]

Dear Leandro,

Thanks for replying!

I had paired ended RNAseq reads (~30 million) which I aligned on the reference genome using STAR, generated a coordinate sorted bam file. Next, I have converted bam to sam and used kisspliceref2genome to call the SNPs.

I am now following the pipeline explained in http://kissplice.prabi.fr/TWAS/. I'll keep you posted about the results!

Regards,

KG