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!
$ 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.
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