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Old 07-22-2012, 02:35 AM   #1
papori
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Location: berd

Join Date: Dec 2010
Posts: 179
Default cufflinks counts vs. rsem counts

Hi all!
i have reference transcriptome with 76,000 contigs that ware built with trinity(DeNovo) from my experiment.
Next, i wanted to know counts per contig.
I started with rsem and i got table of 76,000 contigs with count per contig.
When trying to get count table with cufflinks i got table of 42,000 contigs.
How can it be?
Cufflinks dosent refer to some contigs in purpose?
Any ideas?

Thanks
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