ENCODE database query¶
Input¶
You should have your query bed file.
Usage¶
# login to a compute node
hpcf_interactive.sh
cd to_your_working_dir
ln -s /research_jude/rgs01_jude/groups/chenggrp/projects/blood_regulome/common/atac_footprint/siqi/k562_igd_db/k562_igd_db* .
igd search k562_igd_db.igd -q my.bed -f > out.tsv
Output¶
Each line in the query bed file will be shown as Query chr,start,end in the output table, followed by the overlaped file name
Query chr11, 5268397, 5268664:
0 5268508 5268848 ENCFF388LUX_MLLT1-human.bed
Query chr11, 5268798, 5269050:
0 5268508 5268848 ENCFF388LUX_MLLT1-human.bed
Total overlaps: 2