Question: extract the number of reads around TSS
0
gravatar for Ben
9 weeks ago by
Ben50
Ben50 wrote:

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!

chip-seq • 327 views
ADD COMMENTlink modified 9 weeks ago by Alex Reynolds21k • written 9 weeks ago by Ben50
2
gravatar for Alex Reynolds
9 weeks ago by
Alex Reynolds21k
Seattle, WA USA
Alex Reynolds21k wrote:

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.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Alex Reynolds21k
1
gravatar for h.mon
9 weeks ago by
h.mon9.0k
Brazil
h.mon9.0k wrote:

bam-readcount.

ADD COMMENTlink written 9 weeks ago by h.mon9.0k
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