Question: Are mapped reads between 2 regions common?
gravatar for Mamta
3.4 years ago by
United States
Mamta450 wrote:

Hi all,

I have 2 precursor mirna with similar sequence. Reads map to both the miRNAs. In my alignment setting I did not do unique mapping only. Is there a way to check how many reads are shared between two regions and what might be unique?

Thanks, Mamta

unique reads rnaseq • 758 views
ADD COMMENTlink modified 3.4 years ago by ivivek_ngs4.8k • written 3.4 years ago by Mamta450
gravatar for ivivek_ngs
3.4 years ago by
Seattle,WA, USA
ivivek_ngs4.8k wrote:

Do you have the aligned bam files for both set of sequences? if so then you can give your region of interest and extract the smalls bams for the same region of interest from both the bam files and use bedtools intersect to find the overlap and -v to find unique which accepts bam files as well. for the reads you need to plot the coverage or bam stats for the new bams that you create from the region of interest you are supplying. There are numerous ways you can do. Take a look here.

ADD COMMENTlink written 3.4 years ago by ivivek_ngs4.8k
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