convert gRNA bed file to cutsite bed file¶
usage: to_cutsite_bed.py [-h] [-o OUTPUT] -f INPUT
(--offset OFFSET | --ABE | --CBE)
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
output file name, 4 columns (default: cutsite.bed)
-f INPUT, --input INPUT
input bed file, 6 columns, chr, start, end, seq,
value, strand (default: None)
--offset OFFSET use cas9 cut site (e.g., -3) as gRNA score (default:
None)
--ABE ABE mode not implemented (default: False)
--CBE CBE mode not implemented (default: False)
Summary¶
This program will generate the bed file for cas9 cut positions. User is required to input the offset for Cas9 protein from PAM. spCas9 is -3.
Usage¶
Step 0: Load python version 2.7.13.
module load python/2.7.13
Step 1: Run the command
to_cutsite_bed.py -f gRNA.loci307.bed --offset -3 -o gRNA.cutsite.bed
Input and Output¶
==> gRNA.cutsite.bed <==
chr19 13215439 13215440 CTATGCGCAAGCCCGTGGCC
chr6 135501716 135501717 GACATGTGACAATACGACGG
chr6 135495900 135495901 GCCTGTAATCACAACACTTT
chr6 135376057 135376058 CGCATGCGCACTGCTGTGCA
chr19 12983944 12983945 AGTGGCCAAAGGGGGTGGGT
chr2 58274508 58274509 CGGCTTCTGGGTACCTTCCC
chr6 135376617 135376618 TCTCACTCACTTTGTCGCCC
chr19 13207655 13207656 GGCCCGGGCCGGAGCGTGCC
chr11 4167489 4167490 TTTACTACCTTCGAAAGTTG
chr11 5265111 5265112 AACTGCACACTGGATGGTGG
==> gRNA.loci307.bed <==
chr19 13215423 13215443 CTATGCGCAAGCCCGTGGCC 0 +
chr6 135501700 135501720 GACATGTGACAATACGACGG 0 +
chr6 135495884 135495904 GCCTGTAATCACAACACTTT 0 +
chr6 135376041 135376061 CGCATGCGCACTGCTGTGCA 0 +
chr19 12983928 12983948 AGTGGCCAAAGGGGGTGGGT 0 +
chr2 58274505 58274525 CGGCTTCTGGGTACCTTCCC 0 -
chr6 135376614 135376634 TCTCACTCACTTTGTCGCCC 0 -
chr19 13207639 13207659 GGCCCGGGCCGGAGCGTGCC 0 +
chr11 4167486 4167506 TTTACTACCTTCGAAAGTTG 0 -
chr11 5265108 5265128 AACTGCACACTGGATGGTGG 0 -
Comments¶
code @ github.