Question: Read counts at specific locations in SAM files
gravatar for
19 months ago by
fogarty.mc0 wrote:

I have sam files created using hisat2 of RNAseq reads assembled to a reference of 7 genes (not whole genome). What I need to be able to do is for a given position in the assembly I need too: 1. Count the total # of reads at that position 2. Count of reads of each nucleotide at that position

I have ~30 Rnaseq libraries and ~70 positions I need to assay. This was done in a allohexaploid species so I am looking at positions know to be polymorphic between genomes.

Any ideas of how best to do this?

hisat2 rna-seq sam • 367 views
ADD COMMENTlink written 19 months ago by fogarty.mc0

bam-readcount will do this for you. Samtools depth/mpileup would be other options.

ADD REPLYlink written 19 months ago by genomax90k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1535 users visited in the last hour