General bait design¶
usage: bait_design.py [-h] [-j JID] -f INPUT_BED [-l BAIT_LENGTH] [--src SRC]
[-g GENOME] [--genome_fasta GENOME_FASTA]
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:
bait_design_yli11_2022-03-08)
-f INPUT_BED, --input_bed INPUT_BED
bed file 4 column (default: None)
-l BAIT_LENGTH, --bait_length BAIT_LENGTH
bait_length (default: 120)
--src SRC bait_length (default:
/home/yli11/Programs/BaitsTools/bin/baitstools)
Genome Info:
-g GENOME, --genome GENOME
genome version: hg19, hg38, mm9, mm10, custom. 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)
--genome_fasta GENOME_FASTA
genome fasta file (default:
/home/yli11/Data/Human/hg19/fasta/hg19.fa)
Summary¶
Input a bed file to look for baits. Steps include: (1) general all 120bp baits with stepsize of 50. (2) BLAT all baits to check multi-hits (3) baittools to check for GC and melting TM.
Input¶
chr11 5271034 5271266 HBG1
chr11 5248167 5248406 HBB
Output¶
Usage¶
module load python/2.7.13
bait_design.py -f rick.bed