BedGraph to BigWiggle¶
usage: bdg_to_bw.py [-h] [-j JID] -f BDG_FILES [--data_frame] [-g GENOME]
[-s CHROM_SIZE]
bdg to bw
optional arguments:
-h, --help show this help message and exit
-j JID, --jid JID enter a job ID, which is used to make a new directory.
Every output will be moved into this folder. (default:
bdg_to_bw_yli11_2019-10-10)
-f BDG_FILES, --bdg_files BDG_FILES
bdg file list (default: None)
--data_frame The input is a table, not bdg file list, index and
header are required in this data frame (default:
False)
Genome Info:
-g GENOME, --genome GENOME
genome version: hg19, hg38, mm9, mm10. By default,
specifying a genome version will automatically update
index file, black list, chrom size and
effectiveGenomeSize, unless a user explicitly sets
those options. (default: hg19)
-s CHROM_SIZE, --chrom_size CHROM_SIZE
chrome size (default: /home/yli11/Data/Human/hg19/anno
tations/hg19.chrom.sizes)
Summary¶
Convert bedGraph files to bigWiggle files given genome version. Default is hg19.
Input¶
A list of bdg files.
input.list
----------
CADD.norm.bdg
DeepSEA.norm.bdg
EBM_FDR.norm.bdg
Output¶
BigWiggle files will be generated in the jid folder.
Usage¶
hpcf_interactive
module load python/2.7.13
bdg_to_bw.py -f input.list