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

code @ github.