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Old 02-05-2010, 09:13 AM   #1
DrD2009
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Default Bowtie and Cufflinks

Hello,

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.


Thanks,
Brandon
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Old 02-05-2010, 10:05 AM   #2
mgogol
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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!
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Old 02-05-2010, 10:15 AM   #3
DrD2009
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mgogol, thank you for the reply.

Do you work in bioinformatics here in the Kansas City area? I work at UMKC.
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Old 02-05-2010, 10:17 AM   #4
mgogol
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Yep, I'm at Stowers.
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Old 03-01-2010, 08:44 AM   #5
RockChalkJayhawk
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I'm at KU Med... Looks like KC is representing well.
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Old 03-01-2010, 09:27 AM   #6
mgogol
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I've seen your name around the forum... I went to KU, so it jumped out at me.
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Old 03-01-2010, 09:29 AM   #7
RockChalkJayhawk
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Smile

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.
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Old 03-01-2010, 10:20 AM   #8
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I emailed you...
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Old 03-01-2010, 12:52 PM   #9
DrD2009
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Kansas City seems to be well represented here.
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