how to extract those reads which mapped at 1kb of specific location on chromosomes
1
0
Entering edit mode
7.7 years ago
Raghav ▴ 100

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

hi-c mapped-reads bowtie2 • 1.5k views
ADD COMMENT
1
Entering edit mode
7.7 years ago
cts ★ 1.7k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2369 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6