Empty output file with Kissplice2refgenome

Question

[audrahuffmeyer]

Hi! I am back again with another kissplice related question.

I ran kissplice successfully. The program identified approx 64,000 snps (0a.fa) and approx 1800 alternative splicing events (1.fa). I mapped both files with STAR and then used kissplice2refgenome. I did not get any error notices, as far as I know my kissplice2refgenome runs were successful, but the output files is empty. I see the column headings, but nothing annotated/mapped. All of my snps were in the notmappedreads file. Any recommendations for trouble shooting?

Thank you in advance! Audra

[Pierre Lindenbaum]

Hi! I am back again with another kissplice related question.

C: Kissplice "Finding BCCs" and no output fa or tsv files

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Answer 1

[leandro.ishi.lima]

Hello,

If all of your snps were in the notmappedread file, there could have some reasons (see section 3.1.2 of Kissplice2refgenome's manual: ftp://pbil.univ-lyon1.fr/pub/logiciel/kissplice/tools/kissplice2refgenome_userguide.pdf ): 1) the mapper did not manage to map the SNPs; 2) If you are working with SNPs in paralogous genes, it could be that Kissplice2refgenome filtered them out because they are not mono-locus; 3) Maybe the annotation is not good enough and many SNPs are in unknown genes?

One way to check if STAR managed to map your SNPs is to take a look at the *Log.final.out file. This could give you some idea.

If you do not manage to solve this problem, could you send us the files produced by Kissplice2refgenome, so that we can try to debug (if you need a private channel, you can send your files to leandro <dot> ishi <dot> lima <at> gmail.com . If you do, please warn us here).

Thanks!