Question: Calculate Distribution Of Mapped Reads To Transcriptome Assembly
gravatar for Biojl
5.2 years ago by
Biojl1.6k wrote:


I have a de novo transcriptome assembly done with trinity and afterwards I mapped the reads to it using bowtie2. Does anyone knows of a tool/script to calculate the distribution of the reads in the contigs using the information in the sam file? Basically I would like to know if on average reads map to the beggining or the end of the contigs (~10ā¶ contigs)


ADD COMMENTlink modified 5.2 years ago by hbw70 • written 5.2 years ago by Biojl1.6k
gravatar for hbw
5.2 years ago by
United States
hbw70 wrote:

You could use HTSeq to read in the SAM file and then just count the number of reads mapping to each location. You could then accumulate the reads mapped to each percent length of the transcripts. If you don't mind asking, why would you expect to find more reads in the 3' or 5' end?

ADD COMMENTlink written 5.2 years ago by hbw70

For example low RIN scores are supposed to cause that.

ADD REPLYlink written 5.2 years ago by Biojl1.6k
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