polyoligo-crispr <CHROM:START-END> <OUTPUT> <FASTA/BLASTDB> <OPTIONS>
For a list of all available options and their descriptions, type:
polyoligo-crispr -h
Recommendations (when applicable) are given in the option caption. Note that switches, i.e. boolean options that do not need arguments, have defaults set to
False.
In the following example, CRISPR/Cas9 gRNAs will be designed within the region of interest (ROI):
polyoligo-crispr Fvb2-4:4045000-4045200 out sample_data/blastdb
The software requires three mandatory inputs:
ROI: Target region of interest defined as CHR:START-END.
<OUTPUT>: The base name of the output files.
<FASTA/BLASTDB>: A FASTA file and/or a BLAST database to use as the reference genome. Both file types can be provided by using the same basename. If either is provided, then a conversion will automatically be made to obtain both file types.
Three output files are produced:
<OUTPUT>.log: Log file.
<OUTPUT>.bed: BED file containing the list of designed gRNA. Names are composites of <N_PERFECT_OFFTARGETS>_<N_OFFTARGETS_12MER>_<N_OFFTARGETS_8MER>_<12_MER>_<8_MER>_<TM>_<TTTT> (see below).
<OUTPUT>.txt List of gRNAs with the following columns:
| Column | Description |
|---|---|
CHR |
Chromosome |
START |
Start |
END |
END |
STRAND |
Strand where the gRNA will bind |
SEQ |
gRNA sequence |
PAM |
PAM site |
N_PERFECT_OFFTARGETS |
Number of off-targets with perfect match to the gRNA sequence |
N_OFFTARGETS_12MER |
Number of off-targets with perfect match to 12-MER seed region of the gRNA and no more than 2 mutations elsewhere |
N_OFFTARGETS_8MER |
Number of off-targets with perfect match to 8-MER seed region of the gRNA and no more than 2 mutations elsewhere |
12_MER |
Number of off-targets with perfect match to 12-MER seed region of the gRNA |
8_MER |
Number of off-targets with perfect match to 8-MER seed region of the gRNA |
TM |
Melting temperature of the gRNA |
TTTT |
Does the gRNA contain TTTT repeats. 0=No or 1=Yes. |