extract the number of reads around TSS

Question

[Ben]

I have coded oen python script to extract the amount of reads around TSS from ChIP-seq sam file, but the speed is too slow. Does anyone have any suggestions to solve this question? Thanks in advance!

Answer 1

[Alex Reynolds]

Via BEDOPS:

$ bedmap --echo --count TSSs.bed <(sam2bed < reads.sam) > answer.bed

If you want to pad the TSSs, say by 1k bases on both sides, add the --range N option:

$ bedmap --echo --count --range 1000 TSSs.bed <(sam2bed < reads.sam) > answer.bed

This will likely increase the number of overlaps between reads and (padded) TSSs.

Answer 2

[h.mon]

bam-readcount.