README.md

Prepare references for 4Cseqpipe

Change work directory

Change the work directory to some folder, such as reference/MP_4Cseq_4Cseqpipe, then run the following scripts.

Download reference from the website

bash 01_download_reference.sh

Prepare the template directory

bash 02_prepare_template.sh

Prepare the track database

bash 03_prepare_trackdb.sh

Build restriction site tracks

If you do not know the enzyme restriction site exactly, you can check it on the ReBase website in the IGSuite file.

# First cutter enzyme: HindIII (AAGCTT)
# Second cutter enzyme: DpnII (GATC)
# This script should be run in the current directory!
cd template
perl 4cseqpipe.pl -build_re_db -first_cutter AAGCTT -second_cutters GATC -trackdb_root ../hg19_trackdb
cd ..

Reference

• 4Cseqpipe