Assigning features to a bed file.¶

usage: assign_targets_multi.py [-h] -q QUERY_BED [-tss TSS_BED]
                               --epi_file_list EPI_FILE_LIST [-d1 D1] [-d2 D2]
                               [-d3 D3] [-o OUTPUT] [--label LABEL]

optional arguments:
  -h, --help            show this help message and exit
  -q QUERY_BED, --query_bed QUERY_BED
                        3 column bed file, additional columns are OK, but will
                        be ignored (default: None)
  -tss TSS_BED, --tss_bed TSS_BED
                        4 column bed file, the 4th column should be gene name,
                        should match to the gene name in DEG file (if
                        supplied). Additional columns are OK, but will be
                        ignored (default: None)
  --epi_file_list EPI_FILE_LIST
  -d1 D1                extend query bed for intersection (default: 0)
  -d2 D2                extending tss for intersection (default: 2000)
  -d3 D3                extending epi for intersection (default: 0)
  -o OUTPUT, --output OUTPUT
                        output intermediate file (default: output)
  --label LABEL         prefix for the file (default: TFBS)

Summary¶

This is one of the tools in the target gene assignment workflow, see tf_target_finder pipeline for more details.

Assigned targets will be appended as new columns to the input bed file.

Ref: https://github.com/YichaoOU/TF_target_finder

Input¶

query bed file

A bed file with any number of columns. But the first 3 columns should be chr, start, end.

TSS annotation bed file

hg19: /home/yli11/Data/Human/hg19/Ensembl_v99_2020_Jan/hg19.ensembl.TSS.gene_name.bed

a list of features (bed format: chr, start, end, feature_name)

Use case 1: assigning target genes¶

For promoter capture HiC data, see hg19 pc-HiC.

hpcf_interative.sh

module load conda3

source activate /home/yli11/.conda/envs/py2

assign_targets_multi.py -q input.bed -tss /home/yli11/Data/Human/hg19/Ensembl_v99_2020_Jan/hg19.ensembl.TSS.gene_name.bed --epi_file_list pcHIC.list -o input.bed.assigned_targets.bed

Use case 2: assigning motifs¶

hpcf_interative.sh

module load conda3

source activate /home/yli11/.conda/envs/py2

assign_targets_multi.py -q input.bed -tss /home/yli11/Data/Human/hg19/Ensembl_v99_2020_Jan/hg19.ensembl.TSS.gene_name.bed --epi_file_list /path/to/motif.list -o input.bed.assigned_targets.bed

For hg19, please use:

assign_targets_multi.py -q input.bed -tss /home/yli11/Data/Human/hg19/Ensembl_v99_2020_Jan/hg19.ensembl.TSS.gene_name.bed --epi_file_list /home/yli11/Data/Human/hg19/motif_mapping/motif.list -o input.bed.assigned_targets.bed

For hg38, please use: --epi_file_list /path/to/motif.list

assign_targets_multi.py -q input.bed -tss /home/yli11/Data/Human/hg19/Ensembl_v99_2020_Jan/hg19.ensembl.TSS.gene_name.bed --epi_file_list /home/yli11/Data/Human/hg19/motif_mapping/motif.list -o input.bed.assigned_targets.bed

For mm9, please use: --epi_file_list /path/to/motif.list

assign_targets_multi.py -q input.bed -tss /home/yli11/Data/Human/hg19/Ensembl_v99_2020_Jan/hg19.ensembl.TSS.gene_name.bed --epi_file_list /home/yli11/Data/Human/hg19/motif_mapping/motif.list -o input.bed.assigned_targets.bed

Output¶

-o input.bed.assigned_targets.bed

Comments¶

code @ github.