Long-read sequencing to quantify large indels¶
Input¶
input.tsv to specify input files and sample names¶
# head input.tsv
m84246_250731_201925_s2.hifi_reads.bc1001.bam E26_x
m84246_250731_201925_s2.hifi_reads.bc1002.bam E26_y
m84246_250731_201925_s2.hifi_reads.bc1003.bam E26_yKO
amplicon primer and gRNA cut positions¶
Use IGV BLAT to find your forward and reverse primers start and end locations. --left_primer_start 25234753 --left_primer_end 25236753 --right_primer_start 25242609 --right_primer_end 25244609 ``. Make sure left primer start is the smallest value and right primer end is the largest value. Usually I add +/- 1kb to the primer position. Also your gRNA cut position, ``--gRNA1_cut_pos 25240396 --gRNA2_cut_pos 25240396 --gRNA_cut_flank 2. Here gRNA1 and gRNA2 pos should be the same. This program is designed for HBG promoters that’s why we have 2 gRNA cut sites.
which chr fasta?¶
just map the targeted sequencing data to one chr for faster speed. The location is /research_jude/rgs01_jude/dept/HEM/common/sequencing/chenggrp/pipelines/hg38/fasta/chr_fasta/. In the usage example, it is chr2.
Usage¶
Submit job
run_lsf.py -f input.tsv -p pacbio_count_indel --chr_fasta /research_jude/rgs01_jude/dept/HEM/common/sequencing/chenggrp/pipelines/hg38/fasta/chr_fasta/chr2.fa --left_primer_start 25234753 --left_primer_end 25236753 --right_primer_start 25242609 --right_primer_end 25244609 --gRNA1_cut_pos 25240396 --gRNA2_cut_pos 25240396 --gRNA_cut_flank 2