Exceptionally high peak/reads in ATACseq bam and peak files

0

Entering edit mode

4.5 years ago

bright602 ▴ 50

Hi there, could anyone tell me how to remove the exceptionally high peak in the ATACseq? I got those high reads in both bam files and peak files? Thanks a lot!

enter image description here

sequencing • 1.1k views

ADD COMMENT • link updated 4.5 years ago by i.sudbery 20k • written 4.5 years ago by bright602 ▴ 50

0

Entering edit mode

Can you confirm that you have deduplicated the data and excluded the ENCODE blacklist regions?

ADD REPLY • link 4.5 years ago by i.sudbery 20k

0

Entering edit mode

I removed the PCR duplicates through Picard. For the species I am working on, ENCODE does not have the blacklist regions yet.

ADD REPLY • link 4.5 years ago by bright602 ▴ 50

0

Entering edit mode

Did you set REMOVE_DUPLICATES parameter to true?

ADD REPLY • link 4.5 years ago by GenoMax 147k

1

Entering edit mode

yes, I did set the REMOVE_DUPLICATES=true

ADD REPLY • link 4.5 years ago by bright602 ▴ 50

0

Entering edit mode

Removed mitochondrial reads? Even if not I would ignore it and proceed with downstream analysis and only come back if you see odd things downstream.