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Cnv Mutation Analysis Rna-Seq

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

rna-seq mutation cnv
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updated by Biostar Biostar • written by KS KS

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

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written by Sean Davis Sean Davis

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

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written by KS KS

1 answer

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/

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written by Raygozak Raygozak

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

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written by Sean Davis Sean Davis

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