Question: Cnv Mutation Analysis Rna-Seq
0
gravatar for KS
6.5 years ago by
KS360
KS360 wrote:

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

mutation rna-seq cnv • 3.2k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 6.5 years ago by KS360

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

ADD REPLYlink written 6.5 years ago by Sean Davis25k

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

ADD REPLYlink written 6.5 years ago by KS360

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.

ADD REPLYlink written 6.5 years ago by Sean Davis25k
0
gravatar for Raygozak
6.5 years ago by
Raygozak1.3k
State College, PA, Penn State
Raygozak1.3k wrote:

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/

ADD COMMENTlink written 6.5 years ago by Raygozak1.3k

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

ADD REPLYlink written 6.5 years ago by Sean Davis25k
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