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.

Method ^^^

MCC baits of 120 bp were identified using a 25 bp sliding window at your input target. Candidate baits with multiple genomic occurrences were filtered out using BLAT. Finally, BaitsTools was used to calculate the melting temperature (Tm) of each remaining sequence.

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.