Hello Everyone!
I am new here and new to field of genomics and informatics.
Recently we generated ATAC-seq data of normal and cancer cells.. The data shows open regions in cancer cells compared to normal cells. I would like to know if there is a program out there to generate a list of genes that are in the neighborhood of these open regions. Which I would then feed to IPA or GSEA to see what function those genes enrich for. Ideally I would like to come up three lists , one for genes within 25kb of open regions, 2nd for genes within 75kb and 3rd for genes within 150kb
Please suggest how can I achieve that.
Thank you Alex, I really appreciate your help.
I want to use the release_19 of gencode so i made changes to the above code and was able to successfully generate genes.bed file. But, I couldn't get the "bedmap --echo --echo-map-id-uniq --range 25000 open-regions.bed genes.bed > answer.25kb.bed" code to work. It creates the output file but the contents are just a repeat of open-regions file.
The
--echo
option reports the open region element, the--echo-map-id-uniq
reports all IDs of genes from the Gencode v19 set that overlap the open region.If you want the genes themselves, you could do something like:
Etc.
Leaving out
--echo
and putting in--echo-map
and--multidelim '\n'
options gives you the genes that overlap the open region within 25kb.See the documentation for more information about the
--echo-map-*
options available to you. It might seem a little overwhelming but the docs try to walk through several examples of how they work.Thanks Alex that really helped :)