Question: nomarlizing sequencing depth when use macs2 bdgbroadpeaks
gravatar for langya
18 months ago by
langya50 wrote:


I was wondering when I use macs2 bdgbroadpeaks to call broad peaks on bedgraph file (which is converted from bigwig file that is converted from bam file by our collaborator, don't ask me why they did this and they couldnt find the original bam file), how do I normalize the sequencing depth by million like macs2 callpeak options. And i notice the only output from this is the bed file:

macs2 bdgbroadcall -i --o-prefix

sequencing chip-seq macs2 • 476 views
ADD COMMENTlink written 18 months ago by langya50

It's expecting the input file to be appropriately normalized, if I remember correctly. If you know the original depth (or can at least eye-ball it) then you could use wiggletools to scale the file until you get something reasonable.

ADD REPLYlink written 18 months ago by Devon Ryan92k

they couldnt find the original bam file

can they find the FASTQ files? If not, they'll be in trouble upon submission anyway as they are going to be required by most journals to submit the raw data to a repository

You'll most likely be much better off to re-do the alignment and do things properly

ADD REPLYlink written 18 months ago by Friederike5.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1626 users visited in the last hour