Biostar Beta. Not for public use.
tag density v.s. binding affinity v.s. signal value
1
Entering edit mode
2.5 years ago
liu4gre • 200
United States

I am wondering if it is OK to use signal value stored in narrowPeak format (ENCODE) to represent the binding affinity of a specific TF?

If yes, is this value comparable across samples?

Is it same to tag density?

If not, how can I calculate the binding affinity from narrowPeak file or bam file?

Thanks.

ADD COMMENTlink
1
Entering edit mode
16 months ago
Ying W ♦ 3.9k
South San Francisco, CA

signal.value from narrowPeak is from SPP peak caller

This value is not comparable across samples

It is related to tag density

You can count read overlapping the peaks, see this

Be sure to normalize after you count your reads (peaks have diff sizes and different samples will have different read depths)

See this for more information on what does signal.value mean for ENCODE narrowPeak files: https://sites.google.com/site/anshulkundaje/projects/idr

ADD COMMENTlink
0
Entering edit mode

This is nice. Thanks. So it looks like only RPKM will be a good one to compare across samples...

ADD REPLYlink
0
Entering edit mode

Not the best.. check out this paper

You might want to look into DiffBind or DBChIP if you are interested in differential binding

ADD REPLYlink
0
Entering edit mode

Great. Thanks a lot for the info.

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1