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Old 03-03-2016, 11:06 AM   #4
Location: Vienna

Join Date: Jan 2016
Posts: 10

Originally Posted by SylvainL View Post

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 transcripts...
I mapped directly on my transcription assembly.

I couldn't find any reference to getting the number of reads on each transcript (maybe it's just worded differently?) from the documentation of bedtools. However, I found a Biostars link that suggested using the multicov sub-command in the bedtools suite.

However, according to the documentation the multicov from BEDtools requires genome annotation. For example:

>bedtools multicov –bams run.bam -bed genes.bed

Are you talking about another sub-command or can multicov be run without the bed file?
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