how to extract those reads which mapped at 1kb of specific location on chromosomes

Question

[Raghav]

Dear all,

I have paired end data in form of R1 and R2 of Hi-C library. I mapped these R1 and R2 separately on the reference genome.

Now want extract those reads which mapped on 1 kb from XYZ position on chromosome 1.

Please help me out

yours sincerely

Raghav

Answer 1

[cts]

You can make a bed file for your coordinates of interest and then use the -L option in samtools view to extract the reads from your region of interest.