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Old 11-19-2010, 12:10 PM   #1
Location: Durham

Join Date: Oct 2010
Posts: 19
Default cufflinks with collapsed reads files

Hi Everyone,

We use cufflinks and tophat for our RNA-seq analysis. In our previous protocol, we use FASTX collapser to collapse reads with same sequence into one before doing alignments using bowtie/tophat. Does cufflinks consider such files when calculating FPKM?


Last edited by SongLi; 11-19-2010 at 12:20 PM.
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