I am using plotHeatMap from deeptools to on ChIPseq data to create heatmaps and separate them based on k-means clustering.
This also gives me bed files with peaks based on cluster, and the head of the files look like this:
#chrom start end name score strand thickStart thickEnd itemRGB blockCount blockSizes blockStart deepTools_group 14 27039255 27102509 ENSMUST00000225146 . + 27039255 27102509 0 1 63254 27039253 cluster_1 14 27039078 27089249 ENSMUST00000223942 . + 27039078 27089249 0 1 50171 27039076 cluster_1
When trying to see what genes the names correspond to with a GTF file, they do not correspond to anything since they are away from the transcription start site (can be up to 1kb away). Is there a way I can easily add nearest gene to each row of this bed file?
I have tried the following with no success:
- closest-features from bedops
- bedtools closest
- bedtools intersect my bed file and a GTF file