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Old 06-18-2010, 01:07 PM   #3
Location: USA

Join Date: Apr 2010
Posts: 76

In addition to the reply by Mgogol (which is what I do too)...

1) TopHat and Cufflinks for alignment. Cufflinks gives you FPKM values now instead of the previous RPKM by TopHat, which is mostly the same. Output file in SAM format gives coordinate information i.e. where each read maps onto genome. You can write a simple python script to find out whether the read overlaps any known gene to get read count data for each gene.

2) EdgeR for differential expression. But I think edgeR doesnt work with FPKM data. You need to supply EdgeR with count data to get differential expression.

Hope that helps
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