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