Cnv Mutation Analysis Rna-Seq

Question

[KS]

Hello,

I am analyzing RNA-Seq data of cancer patients using Galaxy Tools. Could any one let me know how to find out CNS or mutations or any indel variants?

Thanks a lot

Kat

[Sean Davis]

Have you used an RNA-seq alignment algorithm that can detect gaps (indels) to map your reads?

[KS]

Yes, I did use Tophat in Galaxy for alignment..

[Sean Davis]

Tophat in galaxy is version 1.x, I believe, so it does not allow indels (since it relies on bowtie and not bowtie2)--http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies. You might want to use tophat2, gsnap, or RUM as other alternatives.

Answer 1

[Raygozak]

Pindel seems to be quite a good program at detecting structural variants (CNVs, large indels, and some other) with short reads. I highly recommend it.

https://trac.nbic.nl/pindel/

[Sean Davis]

Just note that pindel knows nothing of introns, so it might not work as expected on RNA-seq data.