tad-mapping

Topologically-associating domains (TADs) are self-interacting genome regions.
These genomic regions physically interact with each other more frequently than
with regions outside these regions. Because of their self-interacting nature,
it has been hypothesized they function in transcription regulation.

mapping.sh is a script that will get genes that fit a given TAD region. The
script will first take your predefined TAD (chromosome #, start index, end
index), will extract genes (chromosome #, start index, end index, EnsEMBL ID,
description) that fit into the TAD region, pull them from BioMart, and format
them into FASTA.

Note, chromosome location mapping occurs 1000 nucleotides upstream and 50
nucleotides downstream for potential promoter identification using Clover and
MEME-ChIP.

Usage

Requirement:
- OSX or Linux system.

Invoke (in Terminal):
.mapping.sh