Lift Over Bed or bigWiggle files¶
usage: liftover.py [-h] [-o OUTPUT] (--bed BED | --bw BW) [-g GENOME]
[-s CHROM_SIZE] [-c CHAIN_FILE]
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
output file for liftover (default: liftover.bed)
--bed BED input bed file (default: None)
--bw BW Input bw file (default: None)
Genome Info:
-g GENOME, --genome GENOME
Target genome version: hg19, mm10, mm9, hg38 (default:
mm9)
-s CHROM_SIZE, --chrom_size CHROM_SIZE
chrome size (default: /home/yli11/Data/Mouse/mm9/annot
ations/mm9.chrom.sizes)
-c CHAIN_FILE, --chain_file CHAIN_FILE
genome version: hg19, mm10, mm9, hg38 (default: /home/
yli11/Data/Mouse/chain_files/mm10ToMm9.over.chain.gz)
Summary¶
Given a bed or a bw file, convert the genomic coordinates to a target genome version.
Note that -g
is the target genome version. For example, -g mm9
means covert mm10
to mm9
.
Note: same coordinates but with different strand might have error using this script because we use chr:start-end as the key to match new and old files.
Input¶
Bed or BW file.
You can have any number of columns in the bed file. Only chr, start, end columns will be used. Other columns will just stay as before in the output.
Usage¶
hpcf_interactive.sh
module load python/2.7.13
liftover.py --bw GSM1708658_Scl_416B.bw -o GSM1708658_Scl_416B.mm9.bw -g mm9
liftover.py --bed GSM1708658_Scl_416B.bed -o GSM1708658_Scl_416B.mm9.bed -g mm9
For custom genome¶
hpcf_interactive.sh
module load python/2.7.13
liftover.py --bw input.bw -o output.hg19.bw -g custom -c /research/dept/hem/common/sequencing/chenggrp/Phil_custom_genome/d13nt_custom_genome/back_to_hg19.chain -s hg19_main_chrom_size
liftover.py --bed input.bed -o output.mm9.bed -g custom -c /PATH/TO/CUSTOM_CHAIN_file
-s
is not required for --bed
option.
Liftover gff gtf¶
module load crossmap/0.2.4 CrossMap.py gff ~/dirs/genome_browser/yli11/hg19_20copy/hg19_to_20copy.chain hg19.ncbiRefSeq.gtf hg19_20copy.refseq.gtf
sed -i “s/; /; /” hg19_20copy.refseq.gtf
/research/rgs01/resgen/legacy/gb_customTracks/tp/utils/