Peak ident near highly expressed genes

Question

[rbronste]

Hi,

Wondering about a straightforward way to take BED files with peak locations for ChIP-seq data and see where they fall against a list of highly expressed genes (in terms of proximity) from RNA-seq data? Thanks

Rob

[Ben]

Firstly, you need to define the distance, such as promoter, enhancer; then you can judge which peaks are located in the gene feature aboved-mentioned with custome script.

Answer 1

[Sinji]

Probably a more elegant solution available, but:

1. Grab gene locations in BED format. Generally you can do this fairly easily using the UCSC Table Browser and their identifiers option.

2. Use bedops closest-feature with the --dist flag to calculate distances. Make sure to sort files correctly before running this step using bedops sort-bed function or you'll get weird results.