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DrD2009 02-05-2010 09:13 AM

Bowtie and Cufflinks

I have aligned Solexa sequencing data using Bowtie and plan on creating expression profiles using Cufflinks by looking at RPKM values.

There is one thing I am curious about. Is there a way to compare your alignments to annotated regions, so you can give the reads a name along with an RPKM value? I'm assuming Cufflinks simply gives you a read and it's RPKM, what I would like is to be able to see X gene, X miRNA, X puesdogene has an RPKM value of Y.

Is there a way to make this possible? Any suggestions would be great.


mgogol 02-05-2010 10:05 AM

Cufflinks will give you a gene/transcript and its RPKM (if you feed it a gff file). If you don't, it will give you a "made up" gene/transcript and its RPKM.

RPKM is always in terms of a larger genomic entity, not a single read. Reads per kilobase per million.

Hi, fellow Kansas Citian!

DrD2009 02-05-2010 10:15 AM

mgogol, thank you for the reply.

Do you work in bioinformatics here in the Kansas City area? I work at UMKC.

mgogol 02-05-2010 10:17 AM

Yep, I'm at Stowers.

RockChalkJayhawk 03-01-2010 08:44 AM

I'm at KU Med... Looks like KC is representing well.

mgogol 03-01-2010 09:27 AM

I've seen your name around the forum... I went to KU, so it jumped out at me. :)

RockChalkJayhawk 03-01-2010 09:29 AM

We should all get together sometime for lunch. It would be nice to talk face to face with others that actually understand what you are doing.

mgogol 03-01-2010 10:20 AM

I emailed you...

DrD2009 03-01-2010 12:52 PM

Kansas City seems to be well represented here.

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