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Forum: RNA Sequencing 03-07-2016, 11:35 PM
Replies: 8
Views: 3,589
Posted By SylvainL
Hi, since you aligned directly on your...

Hi,

since you aligned directly on your transcriptome, I guess your reference contains all the transcripts, so you can get the counts for each by using samtools idxstats
Forum: RNA Sequencing 03-03-2016, 01:51 AM
Replies: 8
Views: 3,589
Posted By SylvainL
Hi, did you map your reads versus the...

Hi,

did you map your reads versus the closely realted genome of directly on your transcriptome assembly? If you did on the transcriptome, simply use bedtools to get the number of reads on each...
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