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07-22-2012, 02:35 AM
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Senior Member
Location: berd Join Date: Dec 2010
Posts: 179
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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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