This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is There Big Difference Of Using -G Annotation Or Not In Tophat

Hi,

Does anyone try using -G or no -G in tophat mapping. Any effection to the result?

thanks,

Che

tophat
• 2,070 views • link
updated by biorepine biorepine • written by camelbbs camelbbs

2 answers

I would believe the annotation provides more information about exon boundaries and would help in detecting junctions more accurately.

• 0 views • link
written by Raygozak Raygozak

Yes it improves transcriptome assembly. However in my experience the difference is not that big. You can get more information here, RABT assembly

• 0 views • link
written by biorepine biorepine

RABT (and assembly) refers to Cufflinks, but the poster was asking about TopHat.

• 0 views • link
written by Mikael Huss Mikael Huss

yeah. you are right. I will delete my answer. than

• 0 views • link
written by biorepine biorepine

Log in to answer this question.

More posts like this