Calculate Distribution Of Mapped Reads To Transcriptome Assembly

Question

[Biojl]

Hi,

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 (~10⁶ contigs)

Thanks

Answer 1

[hbw]

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?

[Biojl]

For example low RIN scores are supposed to cause that.