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Forum: RNA Sequencing 03-26-2013, 10:59 AM
Replies: 2
Views: 2,128
Posted By JenBarb
I mean a file with defined transcripts and their...

I mean a file with defined transcripts and their corresponding exon coordinates to use with the counting software.

The tophat output gives my reads mapped to the entire genome (mm10 in this case)...
Forum: RNA Sequencing 03-26-2013, 10:24 AM
Replies: 2
Views: 2,128
Posted By JenBarb
Tool for obtaining counts for paired-end strand specific RNAseq data?

Does anyone have any suggestions for software tools to obtain counts for paired-end Strand-specific RNA-seq data? I used Tophat for my genome alignment and need a counting tool now to align to a...
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