extract the number of reads around TSS
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!
• 2,504 views
•
link
updated
by
Alex Reynolds
•
written
by
Ben
•
written
by
Ben
2 answers
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.
• 0 views
•
link
written
by
Alex Reynolds
Log in to answer this question.
More posts like this
-
Faster UMI extraction from scRNA-Seq data
written by paulranum11
-
Are there any tools which can plot biclustered heatmap on ChIP-seq. signal?
written by chiefcat
-
lncRNA machine learning
written by Ben
-
Extract bed file of deletions
written by tassa.saldi •
-
analyze ChIP-chip data
written by Ben
-
parsing bed file
written by a.rex
-
Protocol for Chip-seq analysis for beginners
written by tanni93 •
-
TSS file for D.melanogaster
written by catherine
-
Quick Search For Overlaps With A Mask File
written by diviya.smith •
-
Plotting Reads Around Tss
written by ChIP
