Question: Given a bed file with range of peaks, is it possible to identify the summit of the peak
0
gravatar for oriolebaltimore
5 months ago by
United States
oriolebaltimore130 wrote:

Hello,

Given a bed file with ranges of peaks and corresponding BAM file, can we identify the apex of each peak.

Example:

bed file:

chr1 100 175

chr1 220 235

For first peak 'chr1 100-175' the apex of the peak could be at chr 1 140.

Given the BAM file and bed file, can I get the position of summit for each peak.

Would anyone suggest some trick.

Thanks Adrian.

rna-seq • 201 views
ADD COMMENTlink modified 5 months ago by Alex Reynolds29k • written 5 months ago by oriolebaltimore130
1
gravatar for jared.andrews07
5 months ago by
jared.andrews074.1k
St. Louis, MO
jared.andrews074.1k wrote:

MACS2 has a refinepeak command that can do this in a more intelligent way than just grabbing the max.

ADD COMMENTlink written 5 months ago by jared.andrews074.1k
1
gravatar for oriolebaltimore
5 months ago by
United States
oriolebaltimore130 wrote:

Thanks Jared.

I just found another solution by Pierre. However, that just gives the coverage at the summit but not the position of that summit on chromosome.

Identifying The 'Summit' Coordinate Within Many Coordinates In A Wig File?

ADD COMMENTlink written 5 months ago by oriolebaltimore130
1
gravatar for Alex Reynolds
5 months ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

Maybe the DNase I hotspot calling algorithm here would be of use:

https://github.com/Altius/hotspot2

Hotspot2 counts reads in a BAM file with a sliding window over the genome and identifies "hot" regions of interest, i.e. peaks of fixed or variable widths, with statistical scores that can be used for ranking or other testing.

ADD COMMENTlink written 5 months ago by Alex Reynolds29k
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