Command reference
Full --help for every crisprware subcommand. The module pages cover the options you reach for most; this page is the complete listing.
preprocess_annotation
usage: crisprware preprocess_annotation [-h] -g GTF [-t [TPM_FILES ...]]
[-f {salmon,kallisto,flair,mandalorian,infer}]
[--mean MEAN] [--median MEDIAN]
[--min MIN] [--max MAX] [-n TOP_N]
[-c {median,mean,min,max}]
[-m [{metagene,consensus,longest,shortest} ...]]
[-w TSS_WINDOW TSS_WINDOW]
[-e TES_WINDOW TES_WINDOW]
[-x TX_TO_GENE] [--strip_tx_id]
[-o OUTPUT_DIRECTORY]
Preprocess GTF/GFF annotations with optional RNA-seq filtering.
options:
-h, --help show this help message and exit
-g GTF, --gtf GTF GTF/GFF file to use for isoform filtering.
-t [TPM_FILES ...], --tpm_files [TPM_FILES ...]
A list of one or more isoform quantification files
produced by Salmon, Kallisto or FLAIR (FLAIR outputs
counts, not TPMs). The first column should contain
only the transcript_id and should exactly match the
transcript_ids in --gtf. All transcript_ids in each
TPM file must be common across all files and must be
found in the GTF file.
-f {salmon,kallisto,flair,mandalorian,infer}, --type {salmon,kallisto,flair,mandalorian,infer}
Specify TPM input type. 'infer' guesses the input type
based on the header line. [default: "infer"].
--mean MEAN For a given isoform, the mean tpm/count across samples
must be at least this to be considered, else discard
isoform. [default: 0.0]
--median MEDIAN For a given isoform, the median tpm/count across
samples must be at least this to be considered, else
discard isoform. [default: 0.0]
--min MIN For a given isoform, each sample must have at least
this tpm/count to be considered, else discard isoform.
[default: 0.0]
--max MAX For a given isoform, at least one sample must have at
least this tpm/count to be considered, else discard
isoform. [default: 0.0]
-n TOP_N, --top_n TOP_N
For a given gene, rank all isoforms by median_tpm,
keep the top_n ranked isoforms and discard the rest.
'-1' to keep all isoforms. [default: -1]
-c {median,mean,min,max}, --top_n_column {median,mean,min,max}
The metric by which to rank and filter top isoforms.
Used with '-n' to select expressed transcripts.
[default: median]
-m [{metagene,consensus,longest,shortest} ...], --model [{metagene,consensus,longest,shortest} ...]
Whether to output 'metagene', 'consensus', 'longest',
'shortest' model. 'longest' and 'shortest' select, for
a given gene, the transcript with the longest or
shortest CDS, for now noncoding genes are ignored.
Output is always after tpm filtering has been applied.
Multiple entries are allowed e.g. --model metagene
consensus longest [default: None]
-w TSS_WINDOW TSS_WINDOW, --tss_window TSS_WINDOW TSS_WINDOW
Pass two, space-separated, integers to specifiy the bp
window around the TSS as '<upstream>' '<downstream>'.
Strand-orientation is inferred, i.e. '<upstream>' will
be in the 5' direction of the TSS and <downstream> in
the 3' direction. e.g. --tss_window 250 150. [default:
None]
-e TES_WINDOW TES_WINDOW, --tes_window TES_WINDOW TES_WINDOW
Pass two, space-separated, integers to specifiy the bp
window around the transcription end site, TES, as
'<upstream>' '<downstream>'. Strand-orientation is
inferred, i.e. '<upstream>' will be in the 5'
direction of the TES and <downstream> in the 3'
direction. e.g. --tss_window 0 150. [default: None]
-x TX_TO_GENE, --tx_to_gene TX_TO_GENE
A TSV with transcript IDs in the first column and Gene
IDs in the second. The transcript IDs must match the
first column entries of the --quant_files. If this is
not provided it will be deduced from the GTF/GFF3 and
saved as './tmp/tx2gene.tsv'.
--strip_tx_id Set this flag if there are transcript IDs in the
quantification files but not in the GTF/GFF3.
[default: False]
-o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
Path to output. [default: current directory]
index_genome
usage: crisprware index_genome [-h] -f FASTA [-k [LOCATIONS_TO_KEEP ...]]
[--feature FEATURE]
[-w CONTEXT_WINDOW CONTEXT_WINDOW] -p PAM -l
PROTOSPACER_LENGTH [--pam_5_prime]
[--bin_width BIN_WIDTH] [-o OUTPUT_DIRECTORY]
Build a crispr-ots off-target index (PAM, protospacer length, and PAM
orientation define the enzyme).
options:
-h, --help show this help message and exit
-f FASTA, --fasta FASTA
FASTA file to use as a reference for index creation.
-k [LOCATIONS_TO_KEEP ...], --locations_to_keep [LOCATIONS_TO_KEEP ...]
List of BED/GTF files with coordinates to use for
index creation. These locations will be used for off-
target scoring. If multiple files are passed,
coordinates will be merged with a union operation.
Leave empty to use entire fasta.
--feature FEATURE For any GTF/GFF in '--locations_to_keep', only this
feature will be used for determining appropriate
sgRNA. The feature should match an entry in the third
column of the GTF/GFF. [default: 'transcript']
-w CONTEXT_WINDOW CONTEXT_WINDOW, --context_window CONTEXT_WINDOW CONTEXT_WINDOW
Pass two, space-separated, integers to specifiy the
nucleotide window around the --locations_to_keep
'<upstream>' '<downstream>'. This can be used to
expand the window around the final intervals e.g. '-w
1000 1500' expands chr1 2000 3500 -> chr1 1000 5000
Good for CRISPRi/a [default: 20 20]
-p PAM, --pam PAM PAM motif as an IUPAC string, e.g. NGG (SpCas9), NAG,
TTTV or TTTN (Cas12a). With --protospacer_length and
--pam_5_prime this fully defines the indexed off-
target sites.
-l PROTOSPACER_LENGTH, --protospacer_length PROTOSPACER_LENGTH
Protospacer (spacer) length in bases, e.g. 20 for
SpCas9 or 23 for Cas12a.
--pam_5_prime Set if the PAM is 5' of the protospacer
(Cas12a-style). Omit for a 3' PAM (SpCas9-style).
[default: False]
--bin_width BIN_WIDTH
crispr-ots bin-prefix width (1-15); higher = faster
GPU scan but a larger index. Sweet spots: ~9-10 SpCas9
full-human, 14 for Cas12a full-human on a 24 GB GPU.
[default: engine default]
-o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
Path to output. [default: current directory]
generate_guides
usage: crisprware generate_guides [-h] -f FASTA [-p PAM] [-l SGRNA_LENGTH]
[-w CONTEXT_WINDOW CONTEXT_WINDOW]
[-5 ACTIVE_SITE_OFFSET_5]
[-3 ACTIVE_SITE_OFFSET_3]
[-k [LOCATIONS_TO_KEEP ...]]
[--feature FEATURE]
[--join_operation {merge,intersect}]
[--locations_to_discard [LOCATIONS_TO_DISCARD ...]]
[--prefix PREFIX]
[--gc_range GC_RANGE GC_RANGE]
[--discard_poly_T] [--discard_poly_G]
[--restriction_patterns [RESTRICTION_PATTERNS ...]]
[--flank_5 FLANK_5] [--flank_3 FLANK_3]
[--min_chr_length MIN_CHR_LENGTH]
[--pam_5_prime] [--coords_as_active_site]
[-t THREADS] [--chunk_size CHUNK_SIZE]
[-o OUTPUT_DIRECTORY]
Generate sgRNA sequences matching specified PAM.
options:
-h, --help show this help message and exit
-f FASTA, --fasta FASTA
FASTA file to use as a reference for sgRNA generation.
-p PAM, --pam PAM Protospacer adjacent motif to match. All IUPAC
ambiguity codes are accepted as well as standard ATCG.
[default: NGG]
-l SGRNA_LENGTH, --sgRNA_length SGRNA_LENGTH
Length of sgRNA to generate. [default: 20]
-w CONTEXT_WINDOW CONTEXT_WINDOW, --context_window CONTEXT_WINDOW CONTEXT_WINDOW
Pass two, space-separated, integers to specifiy the
nucleotide window around the sgRNA as '<upstream>'
'<downstream>'. This can be used for downstream
scoring, For Ruleset3 use -w 4 6 to obtain an
appropriate score context. [default: 4 6]
-5 ACTIVE_SITE_OFFSET_5, --active_site_offset_5 ACTIVE_SITE_OFFSET_5
Where cut occurs relative to PAM 5' end. To avoid
error, use '=' sign when passing a negative number,
e.g. --active_site_offset_5=-1 [default: -4]
-3 ACTIVE_SITE_OFFSET_3, --active_site_offset_3 ACTIVE_SITE_OFFSET_3
Where cut occurs relative to PAM 5' end. [default: -2]
To avoid error, use '=' sign when passing a negative
number, e.g. --active_site_offset_3=-3 [default: -4]
-k [LOCATIONS_TO_KEEP ...], --locations_to_keep [LOCATIONS_TO_KEEP ...]
List of BED/GTF files with coordinates in which the
sgRNA desired. If the sgRNA cutsite does not intersect
coordinates in these files they are discarded. Leave
blank to keep all sgRNA. e.g. atac_peak.bed genes.gtf
--feature FEATURE For any GTF/GFF in '--locations_to_keep', only this
feature will be used for determining appropriate
sgRNA. The feature should match an entry in the third
column of the GTF/GFF. [default: 'exon']
--join_operation {merge,intersect}
How to treat '--locations_to_keep' if multiple files
are passed. Either 'merge' or 'intersect' can be used
and work as described in Bedtools. If 'merge', sgRNA
will be kept if its cutsite intersects an entry in ANY
of the files, if 'intersect' the cutsite must
intersect an entry in EACH file. [default:
'intersect']
--locations_to_discard [LOCATIONS_TO_DISCARD ...]
List of BED/GTF files with coordinates where sgRNA
should not target. If the sgRNA cutsite intersects
coordinates in these files the sgRNA is discarded.
Leave blank to keep all sgRNA. e.g. TSS.bed
coding_genes.gtf
--prefix PREFIX Prefix to use for sgRNA identifiers. [default: None]
--gc_range GC_RANGE GC_RANGE
Pass two, space-separated, integers to specifiy the
percentile range of GC content e.g. '--gc_range 25
75'. [default: 0 100]
--discard_poly_T Whether to discard polyT (>TTT) sgRNA. Recommend True
for PolIII promoters [default: False]
--discard_poly_G Whether to discard polyT (>GGGG) sgRNA. [default:
False]
--restriction_patterns [RESTRICTION_PATTERNS ...]
Reject sgRNA with these restriction patterns. Also
checks 5'flank+sgRNA+3'flank, and reverse complement,
if provided. For multiple values, separate by space.
e.g. GCGGCCGC TCTAGA CACCTGC
--flank_5 FLANK_5 include the 5' context of the lentivirus vector. Used
in conjunction with --restriction_patterns to remove
incompatible sgRNA
--flank_3 FLANK_3 include the 3' context of the lentivirus vector. Used
in conjunction with --restriction_patterns to remove
incompatible sgRNA
--min_chr_length MIN_CHR_LENGTH
Minimum chromosome length to consider for sgRNA
generation. [default: 20]
--pam_5_prime If the PAM is positioned 5' to the protospacer set
this flag, e.g. for Cas12a sgRNAs [default: False]
--coords_as_active_site
Whether to output bed coordinates at the active site
rather than the coordinates of the entire protospacer.
For purposes of keeping or discarding sgRNAs, overlap
with the active site coordinates will be used
regardless [default: True]
-t THREADS, --threads THREADS
Number of worker processes. Parallelism scales with
the number of genome windows (see --chunk_size), not
the PAM count, so this can usefully exceed it.
[default: 4]
--chunk_size CHUNK_SIZE
Genome window size in bp for parallel scanning;
smaller = more/finer tasks (better load balance,
slightly more overhead). [default: 5,000,000]
-o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
Path to output. [default: current directory]
score_guides
usage: crisprware score_guides [-h] -b GRNA_BED [-i [GUIDESCAN2_INDICES ...]]
[--tracr {Hsu2013,Chen2013,both}] [-t THREADS]
[--threshold THRESHOLD]
[--mismatches MISMATCHES]
[--rna_bulges RNA_BULGES]
[--dna_bulges DNA_BULGES]
[--mode {succinct,complete}]
[--alt_pams [ALT_PAMS ...]] [-d] [--skip_rs3]
[--skip_gs2] [--min_rs3 MIN_RS3]
[--cas12a_scorer {none,enpam_gb,deepcpf1,enseq_deepcpf1,seq_deepcpf1variants,both} [{none,enpam_gb,deepcpf1,enseq_deepcpf1,seq_deepcpf1variants,both} ...]]
[--cas12a_variant CAS12A_VARIANT]
[--min_deepcpf1 MIN_DEEPCPF1]
[--min_enpam_gb MIN_ENPAM_GB]
[--min_enseq_deepcpf1 MIN_ENSEQ_DEEPCPF1]
[--cas9_scorer {none,deepspcas9,deephf_wt_u6,deephf_esp,deephf_hf} [{none,deepspcas9,deephf_wt_u6,deephf_esp,deephf_hf} ...]]
[--min_deepspcas9 MIN_DEEPSPCAS9]
[--min_deephf MIN_DEEPHF]
[--chunk_size CHUNK_SIZE] [-k]
[-o OUTPUT_DIRECTORY] [--ucscgb UCSCGB]
[--chrom_sizes CHROM_SIZES]
[--crispr_ots_bin CRISPR_OTS_BIN]
[--ucscgb_scanner {gpu,cpu}]
[--ucscgb_cfd_threshold UCSCGB_CFD_THRESHOLD]
[--ucscgb_list_cap UCSCGB_LIST_CAP]
[--ucscgb_blank_threshold UCSCGB_BLANK_THRESHOLD]
[--ucscgb_reuse_offtargets]
[--ucscgb_2xnls | --no-ucscgb_2xnls]
[--ucscgb_chunk_max UCSCGB_CHUNK_MAX]
[--ucscgb_gpus UCSCGB_GPUS]
[--ucscgb_keep_chunks]
Score guides with RS3 cleavage and crispr-ots/Guidescan2 off-target
specificity.
options:
-h, --help show this help message and exit
-b GRNA_BED, --grna_bed GRNA_BED
grnas.bed ouput of generate_guides.
-i [GUIDESCAN2_INDICES ...], --guidescan2_indices [GUIDESCAN2_INDICES ...]
One or more, space-separate Guidescan2 indices. A
specificity score will be calculated against each
index separately.
--tracr {Hsu2013,Chen2013,both}
TracrRNA version for cleavage scoring. Either
'Hsu2013' or 'Chen2013' or 'both', see
https://github.com/gpp-rnd/rs3 for details.
-t THREADS, --threads THREADS
Number of threads [default: 8]
--threshold THRESHOLD
Threshold for Guidescan2 off-target hits. If off-
targets are found this distance away the gRNA will be
discarded, i.e. set to 2 to discard any guides with a
0, 1 or 2 mismatches from another PAM adjacent
sequence. --threshold=-1 to retain all guides
[default: 2]
--mismatches MISMATCHES
Number of mismatches for Guidescan2 off-target scoring
[default: 3]
--rna_bulges RNA_BULGES
RNA bulges for Guidescan2 off-target scoring [default:
0]
--dna_bulges DNA_BULGES
DNA bulges for Guidescan2 off-target scoring [default:
0]
--mode {succinct,complete}
Whether Guidescan2 temporary output should be succinct
or complete mode [default: 0]
--alt_pams [ALT_PAMS ...]
One or more, space-separate alternative pams for off-
target consideration. e.g. NAG
-d, --drop_duplicates
Drop exact duplicate gRNAs before scoring to save
time. Set flag to retain duplicates. [default: True]
--skip_rs3 Set flag to skip RS3 scoring [default: False]
--skip_gs2 Set flag to skip Guidescan2 scoring [default: False]
--min_rs3 MIN_RS3 Minimum cleavage RS3 score. RS3 cleavage scores are
formatted as z-scores, so this is interpreted as a
standard deviation cutoff. Functionality also
available in rank_guides.py. Applying at this stage
can increase speed by filtering before off-target
scoring. [default: None]
--cas12a_scorer {none,enpam_gb,deepcpf1,enseq_deepcpf1,seq_deepcpf1variants,both} [{none,enpam_gb,deepcpf1,enseq_deepcpf1,seq_deepcpf1variants,both} ...]
One or more Cas12a on-target scorers (space-
separated). enpam_gb for en(As)Cas12a; deepcpf1 for
wildtype AsCas12a/LbCas12a (Kim 2018); enseq_deepcpf1
for wildtype AsCas12a (Chen 2025, modern);
seq_deepcpf1variants for variant-specific scoring
(requires --cas12a_variant). 'both' is the legacy
alias for 'enpam_gb deepcpf1'. Multiple values may be
combined (e.g. --cas12a_scorer enpam_gb deepcpf1
enseq_deepcpf1). Mutually exclusive with --tracr (RS3
is SpCas9-only); implies --skip_rs3. [default: none]
--cas12a_variant CAS12A_VARIANT
Cas12a variant name (e.g. AsCas12a_Ultra,
enAsCas12a-HF1, LbCas12a, HyperFi-AsCas12a). Required
when --cas12a_scorer is seq_deepcpf1variants. See
crisprware.scorers.seq_deepcpf1variants for the full
23-variant list.
--min_deepcpf1 MIN_DEEPCPF1
Minimum DeepCpf1 score (raw regression, ~[0, 100]).
Applied after scoring; analogous to --min_rs3.
[default: None]
--min_enpam_gb MIN_ENPAM_GB
Minimum enPAM+GB score (probability-like, [0, 1]).
Applied after scoring; analogous to --min_rs3.
[default: None]
--min_enseq_deepcpf1 MIN_ENSEQ_DEEPCPF1
Minimum enseq-DeepCpf1 / seq-DeepCpf1variants score
(probability, [0, 1]). Applied after scoring.
[default: None]
--cas9_scorer {none,deepspcas9,deephf_wt_u6,deephf_esp,deephf_hf} [{none,deepspcas9,deephf_wt_u6,deephf_esp,deephf_hf} ...]
One or more additional SpCas9 on-target scorers
(space-separated) to run alongside RS3. deepspcas9:
Kim 2019 inception-CNN (Sci Adv); 30-nt context (4 +
20 protospacer + 3 PAM + 3 downstream); unbounded
regression. deephf_*: Wang 2019 BiLSTM (Nat Commun)
for three Cas9 variants -- wildtype SpCas9 (wt_u6),
eSpCas9 (esp), SpCas9-HF1 (hf); 23-nt protospacer+PAM
input; output in [0, 1]. Multiple values may be
combined (e.g. --cas9_scorer deepspcas9 deephf_wt_u6
deephf_esp deephf_hf). Runs in parallel with --tracr
(no mutex). [default: none]
--min_deepspcas9 MIN_DEEPSPCAS9
Minimum DeepSpCas9 score (unbounded regression, ~[0,
100]). Applied after scoring; analogous to --min_rs3.
[default: None]
--min_deephf MIN_DEEPHF
Minimum DeepHF score (probability, [0, 1]). Applied to
whichever deephf_* variant is selected. [default:
None]
--chunk_size CHUNK_SIZE
Number of gRNAs to hold in memory for cleavage scoring
and off-target filtering. Reduce if memory
constrained. Increasing may improve runtime [default:
100000]
-k, --keep_tmp Set flag to keep temporary Guidescan2 output [default:
False]
-o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
Path to output. [default: current directory]
UCSC browser track (Cas12a):
--ucscgb UCSCGB Alternative output path: write a UCSC Genome Browser
Cas12a track (cas12a.bb, crisprDetails.tab.gz + .gzi,
cas12aTargets.as) to this directory. Runs the selected
--cas12a_scorer on-target models plus a streaming
crispr-ots off-target pass (--output-mode both,
skipping off-targets for perfect-match guides) against
the first -i index. Implies Cas12a mode and retains
duplicate guides. [default: None]
--chrom_sizes CHROM_SIZES
chrom.sizes file (chrom<TAB>size) for bedToBigBed when
--ucscgb is set.
--crispr_ots_bin CRISPR_OTS_BIN
Path to the crispr-ots binary used for the --ucscgb
streaming pass (must support --output-mode/--scanner;
default: 'crispr-ots' on PATH).
--ucscgb_scanner {gpu,cpu}
Scanner for the --ucscgb off-target pass [default:
gpu].
--ucscgb_cfd_threshold UCSCGB_CFD_THRESHOLD
CFD floor for the off-target list written to
crisprDetails (counts are unaffected — they come from
the unfloored Mode-1 totals). [default: 0.023]
--ucscgb_list_cap UCSCGB_LIST_CAP
Max off-targets listed per guide in crisprDetails (top
by score) [default: 100].
--ucscgb_blank_threshold UCSCGB_BLANK_THRESHOLD
Guides with more than this many off-targets get an
empty list (counts kept) — the viewer shows 'Too many
off-targets'. [default: 2000]
--ucscgb_reuse_offtargets
Reuse an existing off-target enumerate output
(offtargets.csv + .ot.tsv) in the --ucscgb dir instead
of re-running crispr-ots. Use when re-assembling a
track after an adapter-only change (the engine output
is unchanged), skipping the GPU pass. [default: off]
--ucscgb_2xnls, --no-ucscgb_2xnls
Also score off-targets with the 2xNLS-Cas12a matrix
and emit its TTTV/TTTN specificity columns (a second,
aggregated off-target pass — the off-target list still
comes from the enCas12a pass). [default: on; use --no-
ucscgb_2xnls to skip]
--ucscgb_chunk_max UCSCGB_CHUNK_MAX
If >0, build the track in chunks of at most this many
guides and merge the per-chunk tracks into one
(recomputing crisprDetails.tab byte offsets). Bounds
peak memory and disk, and enables multi-GPU fan-out
via --ucscgb_gpus. 0 = single pass over all guides.
[default: 0]
--ucscgb_gpus UCSCGB_GPUS
Comma-separated CUDA device ids to fan
--ucscgb_chunk_max chunks across (e.g.
'0,1,2,3,4,5,6,7'); each concurrent chunk's off-target
pass is pinned to one device, so chunks never share a
GPU. Only used when --ucscgb_chunk_max>0. [default:
single device 0].
--ucscgb_keep_chunks Keep the per-chunk working dir (<ucscgb>/chunks/)
after merging, for inspection or resume. [default:
delete after a successful merge].
rank_guides
usage: crisprware rank_guides [-h] -k SCORED_GUIDES -t TARGETS
[--target_mode {gene,tx}] [-f FEATURE]
[-p PERCENTILE_RANGE PERCENTILE_RANGE]
[-n NUMBER_OF_GUIDES]
[--min_spacing MIN_SPACING] [--output_all]
[--plot_histogram] [-c [FILTERING_COLUMNS ...]]
[-m [MINIMUM_VALUES ...]]
[-r [RANKING_COLUMNS ...]]
[-w [COLUMN_WEIGHTS ...]] [--normalize_columns]
[-o OUTPUT_DIRECTORY]
Rank and select best guides based on scoring criteria.
options:
-h, --help show this help message and exit
-k SCORED_GUIDES, --scored_guides SCORED_GUIDES
<score_guides_output>.bed output from score_guides.
-t TARGETS, --targets TARGETS
BED/GTF/GFF used to select final guides per target.
For GTF/GFF, set --target_mode to either 'gene' or
'tx'. For BED, targets are each entry. Use '--
number_of_targets' to set the number of guides chosen
for each target.
--target_mode {gene,tx}
If a GTF/GFF is used to select targets, gRNAs can be
grouped at either the 'tx' or 'gene' level e.g. '--
target_mode gene -n 10' chooses 10 guides per gene, '
--target_mode tx -n 10' chooses 10 per transcript
[default: gene].
-f FEATURE, --feature FEATURE
If GTF/GFF passed, use this feature for processing
e.g. 'exon', 'CDS', '5UTR', etc. The feature appears
in the third column of the GTF/GFF [default: CDS].
-p PERCENTILE_RANGE PERCENTILE_RANGE, --percentile_range PERCENTILE_RANGE PERCENTILE_RANGE
Allowable range of guide for each transcript and
feature set, e.g. '-p 60 80 -f exon' returns gRNAs in
the 60th to 80th percentile of exons for a given
transcript. Default setting returns guides anywhere in
the CDS for each transcript [default: 0 100]
-n NUMBER_OF_GUIDES, --number_of_guides NUMBER_OF_GUIDES
Number of guides returned per target.'-1' to keep all
guides [default: -1]
--min_spacing MIN_SPACING
The minimum nucleotide space between guides for a
given target. e.g. --min_spacing 10, requires guides
10 nts appart. 0 to allow overlapping guides.[default:
0]
--output_all Set flag to save gRNA-target TSVs at each stage of
filtering rather than just the end.[default: False]
--plot_histogram Set flag to plot a histogram of the distribution of
gRNAs per target after each filtering step. Sets '--
output_all' to True.[default: False]
-c [FILTERING_COLUMNS ...], --filtering_columns [FILTERING_COLUMNS ...]
One or more space-separated column names used for
filtering. Uses raw values. e.g. '-c rs3_z_score
specificity_Hg38_index'.
-m [MINIMUM_VALUES ...], --minimum_values [MINIMUM_VALUES ...]
A space-separated list of minimum values for each
column in passed by --ranking_columns. e.g. '-c
rs3_z_score specificity_Hg38_index -m "-1" 0.2'
Default is no minimum [default: None]
-r [RANKING_COLUMNS ...], --ranking_columns [RANKING_COLUMNS ...]
One or more space-separated column names used for
guide ranking. e.g. '-r rs3_score_Hsu2013
rs3_score_Chen2013'.
-w [COLUMN_WEIGHTS ...], --column_weights [COLUMN_WEIGHTS ...]
A space-separated list of weight values for each
column in passed by --ranking_columns. e.g. '-c
rs3_score specificity_Hg38_index -w 1 0' Default is
equal weighting for all ranking columns.
--normalize_columns Scale ranking column values to 0 to 1 [default: True]
-o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
Path to output. [default: current directory]