Samtools to extract reads in a region for a Hi-C experiment

Question

[manuel.fernandez]

Hi everyone,

I'm trying to extract the reads with BOTH ends mapped to a specific region of Chr 12 (6,140,000 - 8,460,000) in a capture Hi-C experiment. I'm using the following command in samtools:

samtools view $file.bam -h "chr12:6140000-8460000"

It seems to work fine for the first read, but there are many second ends that are mapped to regions outside, even in other chromosomes, i.e., I get something like this:

ERR5035850.12056960     130      chr12   6142560 0       76P     =          6142773          76      *        *       TC:i:1  S1:i:1  S2:i:0
ERR5035850.2480369       128      chr12   6142560 0       76P     =          6144648          76      *        *       TC:i:1  S1:i:0  S2:i:0
ERR5035850.76070047     1152    chr12   6142560 0       76P     chr16   19345512        76       *       *       TC:i:1  S1:i:1  S2:i:1
ERR5035850.2336828       152      chr12   6142560 0       76P     =          6142785          76      *        *       TC:i:1  S1:i:1  S2:i:0

I have also tried including the flag -f 2, and these unwanted regions seem to go away, but I'm not completely sure this is the flag I want to use for a Hi-C experiment.

Could anyone help me a bit on this?

Thanks a lot!

Manuel F. Merino