Question: Peak ident near highly expressed genes
0
gravatar for rbronste
3.0 years ago by
rbronste360
rbronste360 wrote:

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

rna-seq chip-seq bedops • 667 views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by rbronste360

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.

ADD REPLYlink written 3.0 years ago by Ben50
1
gravatar for Sinji
3.0 years ago by
Sinji3.0k
UT Southwestern Medical Center
Sinji3.0k wrote:

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.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Sinji3.0k
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