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Peak ident near highly expressed genes

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

chip-seq rna-seq bedops
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written by rbronste rbronste

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.

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written by Ben Ben

1 answer

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.

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written by Sinji Sinji

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