I have a bedGraph file from a ChIP-seq experiment (H3K27me3) downloaded from GEO (GSE84324). I want to obtain a list of genes with this mark enriched. However, the bedGraph shows a continuous signal with adjacent regions while I was expecting selected regions where I just needed to annotate genes.
I've read in the corresponding paper that they used HOMER for generating the bedGraph:
makeUCSCfile out_dir –o out.bdg –name sample_name -color track_color –fragLength 150 –avg -fsize 1e20
I am quite new to ChIP-seq analysis and need some advice here on how to proceed. My thoughts are:
a) Use MACS2 bdgbroadcall using the bedGraph as input. Problem: bedGraph has not been generated with MACS/MACS2.
b) Use ScoreMatrixBin from R (genomation package) to get an score on all promoters and then apply a cutoff to identify peaks (in the original paper, they proceed like this). This may be a naive approach....
c) Try to obtain the ChIP-seq raw data and repeat the analysis.
Please, could you give me some advice? Any other proposal is welcome.
Thanks in advance!