Question: Annotation of ChIP-seq peaks after MACS
1
gravatar for dorota.komar
10 months ago by
dorota.komar10
dorota.komar10 wrote:

Hi everyone, I am trying to understand the problem I have when trying to annotate the peaks of my ChIP-seq that I got after MACS. I am using "operate on genomic intervals" tool to join bed file after MACS and the reference genome in gff3 (Arabidopsis TAIR10) format (that galaxy automatically treats as bed), but I cannot process this step, because the info "All datasets must belong to same genomic build, this dataset is linked to build '?' " is showed. What does it mean? Does it mean the reference genome is somehow incompatibile with the MACS reads? I used the built in galaxy TAIR10 genome and for the annotation a separate file that I downloaded from TAIR, but there should not be any difference between them, should there? Please help!

peak annotation chip-seq macs • 1.6k views
ADD COMMENTlink modified 10 months ago by meer.k.mustafa0 • written 10 months ago by dorota.komar10
3
gravatar for EagleEye
10 months ago by
EagleEye4.9k
Sweden
EagleEye4.9k wrote:

Try Homer annotate peaks with your custom annotation file (gff3).

http://homer.ucsd.edu/homer/ngs/annotation.html

ADD COMMENTlink written 10 months ago by EagleEye4.9k
1
gravatar for Alex Reynolds
10 months ago by
Alex Reynolds22k
Seattle, WA USA
Alex Reynolds22k wrote:

You can use BEDOPS bedmap and gff2bed to map TAIR10 annotations (or annotations from any reference genome you have a GFF file for) to ChIP-seq peaks, i.e.:

$ bedmap --echo --echo-map peaks.bed <(gff2bed < annotations.gff) > answer.bed

If you don't need the entire annotation, you can use --echo-map-id or other --echo-map-* options to get a subset of the annotation data.

ADD COMMENTlink modified 10 months ago • written 10 months ago by Alex Reynolds22k
0
gravatar for dorota.komar
10 months ago by
dorota.komar10
dorota.komar10 wrote:

Can it be happening, because in my bed file i have chromosom name strating with lower case and in the reference genome with upper case?

ADD COMMENTlink written 10 months ago by dorota.komar10

Maybe you can use this package ChIPpeakAnno

ADD REPLYlink written 10 months ago by zjhzwang180
0
gravatar for meer.k.mustafa
10 months ago by
meer.k.mustafa0 wrote:

You can also annotate your peaks using a simple closestBED -a peaks.bed -b genes_with_coordinates_annotation.bed

This would allow you to annotate your peaks with any coordinate-description (gene, CTCF site, etc..) file.

ADD COMMENTlink written 10 months ago by meer.k.mustafa0
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