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Thread | Thread Starter | Forum | Replies | Last Post |
problems with zero counts using cufflinks | yaaraore | Bioinformatics | 1 | 08-07-2013 05:52 AM |
RSEM expected counts question | tboothby | Bioinformatics | 2 | 01-26-2012 04:45 AM |
DESeq: Read counts vs. BP counts | burkard | Bioinformatics | 0 | 08-05-2010 11:52 PM |
Cufflinks convert FPKM to Read Counts | zee | Bioinformatics | 0 | 03-08-2010 06:35 PM |
How to convert cufflinks output to raw counts | jebe | RNA Sequencing | 0 | 01-26-2010 11:29 AM |
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#1 |
Senior Member
Location: berd Join Date: Dec 2010
Posts: 179
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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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