Annotation of ChIP-seq peaks after MACS

Question

[dorota.komar]

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!

Answer 1

[EagleEye]

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

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

Answer 2

[Alex Reynolds]

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. See the documentation or bedmap --help for more detail.

Answer 3

[dorota.komar]

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?

[zjhzwang]

Maybe you can use this package ChIPpeakAnno

Answer 4

[meer.k.mustafa]

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.