Are mapped reads between 2 regions common?

Question

[datanerd]

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

Answer 1

[ivivek_ngs]

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.