Query bed overlap with a list of bed files¶
Summary¶
The goal is to look at the percentage of overlap of your region of interest in a list of bed files. For example, we have a N chip-seq peaks, we would like to know if these N peaks remain in open chromatin across the whole blood lineage. Then, the N peaks is your query list, and the list of bed files is your reference list.
Input¶
There are two input files. The first in your query list, the second is your reference list.
Query Bed¶
Input is a bed file (chr, start, end, additional columns are not used), e.g., query.bed
Reference list¶
Input is a file contaning a list of bed files, e.g., peak.list
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/B.ImmGen.mm10.ATAC.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/CMP.ENCODE.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/DC.ImmGen.mm10.ATAC.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/Ery.ENCODE.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/GMP.ENCODE.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/HSC.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/MEP.ENCODE.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/MK.ENCODE.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/MKP.ENCODE.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/Mono.ENCODE.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/MPP.ImmGen.mm10.ATAC.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/Neutro.ENCODE.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/NK.ImmGen.mm10.ATAC.mm9.bed
/home/yli11/Data/Mouse/mouse_blood/mm9_blood_ATAC/T.ImmGen.mm10.ATAC.mm9.bed
Usage¶
module load python/2.7.13
# for mm9
bedlist_overlap.py query.bed /home/yli11/Data/Mouse/mouse_blood/peak.list
# for hg19
bedlist_overlap.py query.bed /home/yli11/Data/Human/hg19/annotations/blood.peaks.list
## for mm9 data visualization
plot_blood_lineage.py --svg_template /home/yli11/HemTools/share/misc/mouse_blood.svg -f peak_overlap_percent.tsv
## for hg19 data visualization
plot_blood_lineage.py --svg_template /home/yli11/HemTools/share/misc/blood_lineage_Hchang_13cells.svg -f peak_overlap_percent.tsv
Output¶
The percentage of overlap (percentage in terms of query size) is provided in file peak_overlap_percent.tsv, this file can be directly used to plot_blood_lineage.py.
The my_overlap_matrix.tsv file is a binary matrix with each row being your query peak and each column being the reference bed file (class)