Unique interval among two bed files

Question

[kanwarjag]

I have two Chip seq bed files with genomic coordinates one is from control and second is from pull down (treated). These files are from GEO and no other information is available. I want to identify unique non-overlapping coordinates in second (treated) bed file as compared to first file. I know I can use intersect, Bed tool to find overlapping regions. How should I find out non-overlapping unique regions enriched in treated file.

Thanks

Answer 1

[rpolicastro]

One option is to use the -v argument of bedtools intersect which will return peaks that have no overlapping regions with the control peaks. Your second option would be to use bedtools subtract to subtract out from the experimental peaks parts that overlap with the control peaks.

Taking a step back for a second, usually a GEO entry will have an associated SRA accession, in which case you could download the fastq files, processes them, and then use MACS2 to properly call the peaks in the experimental condition using the control.