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Old 09-24-2013, 07:02 PM   #1
AdrianP
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Default Quick RPKM?

Hello,

I have a classic scenario where i have a bunch of predicted genes, and RNA-Seq data. I want RPKM for each gene, and I have the genes in a fasta file.

Suppose I align the reads to the genes using bowtie. What next? Any script to determine RPKM for each gene and sort the genes by RPKM values?

Thank you,
Adrian
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Old 09-24-2013, 08:01 PM   #2
ThePresident
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I used bowtie to align my reads and cufflinks to extract RPKM values...
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Old 09-24-2013, 08:17 PM   #3
AdrianP
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Would you mind sharing your command line to do that? Given any .bam file.
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Old 09-24-2013, 08:26 PM   #4
ThePresident
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Oh my... It's been a while and I can't remember exactly and to be honest, I'm in the middle of an analysis. However, you'll find a manual here: cufflinks.cbcb.umd.edu/manual.html

TP
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Old 09-25-2013, 03:15 AM   #5
a_mt
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Hi Adrian,

There's a qucik way to do it:

1. convert your SAM/BAM to wiggle file (you can use bedtools or check this)

2. multiply every value in wiggle by (1,000,000/no. of reads)

for eg: if you have 150 million reads, (1,000,000/150,000,000) would be 0.006666

So multiply every wiggle by 0.00666 !

Source: I read about this a long back on a blog. I dont remember the link though :P
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