giftwrap-count
The giftwrap-count command is used to map GIFT-seq reads to the probe set into a flat file. This command is typically run after the initial sequencing data has been generated and is essential for quantifying the expression of genes or other targets in the GIFT-seq workflow.
giftwrap-count --helpUsage: giftwrap-count [-h] [--version] --probes PROBES
[--trim_probes TRIM_PROBES] [-r1 READ1] [-r2 READ2]
[--unmapped_reads UNMAPPED_READS]
[--flexible_start_mapping] [--project PROJECT] -o OUTPUT
[-c CORES] [-n N_READS_PER_BATCH] [-t THRESHOLD]
[--technology {Flex,Flex-v2,Flex-v2-R1,VisiumHD,Visium-v1,Visium-v2,Visium-v3,Visium-v4,Visium-v5,Custom}]
[--tech_def TECH_DEF] [--overwrite]
[--multiplex MULTIPLEX] [--barcode BARCODE]
[--r1_length R1_LENGTH] [--r2_length R2_LENGTH]
[--allow_indels] [--skip_constant_seq]
[--allow_any_combination]
[--cellranger_output CELLRANGER_OUTPUT]
[--expected_gap_length EXPECTED_GAP_LENGTH]
Quantify the genotypes of Gap-filling probes.
Options:
-h, --help show this help message and exit
--version, -v Show the version of the GIFTwrap pipeline.
--probes, -p PROBES Path to the generated gap-filling probe set file.
--trim_probes TRIM_PROBES
If > 0, trim the probes to the given length before
mapping. This can be useful if the probes have a
common sequence at the end that is not expected to be
sequenced. If the probe file contains expected
gapfills, this will be used to inform the trimming.
-r1, --read1 READ1 Path to the R1 file. Either the fastq/fastq.gz file,
or a file prefix to find a set of files.
-r2, --read2 READ2 Path to the R2 file. Either the fastq/fastq.gz file,
or a file prefix to find a set of files.
--unmapped_reads UNMAPPED_READS
If provided, unmapped reads are written to the file
prefix given.
--flexible_start_mapping
If set, we no longer assume that the R2 read starts
with the LHS probe and that there may be an insertion
that would need to be trimmed.
--project PROJECT The generic name for the project. Used to
automatically find R1 and R2 fastq files. Mutually
exclusive with -r1 and -r2 arguments.
-o, --output OUTPUT Name of the output directory.
-c, --cores CORES The number of cores to use. Less than 1 defaults to
the number of available cores.
-n, --n_reads_per_batch N_READS_PER_BATCH
The number of reads to process in a batch. Defaults to
10 million
-t, --threshold THRESHOLD
The maximum edit distance for fuzzy matching probes
and cell barcodes per 10bp.
--technology, -e {Flex,Flex-v2,Flex-v2-R1,VisiumHD,Visium-v1,Visium-v2,Visium-v3,Visium-v4,Visium-v5,Custom}
The technology used to generate the gap-filling
probes. Default is Flex. If 'Custom', you must provide
the --tech_def argument.
--tech_def TECH_DEF The path to the technology definition python file to
import. Must include a single class definition that
inherits from TechnologyFormatInfo.
--overwrite, -f Overwrite the output directory if it exists.
--multiplex, -m MULTIPLEX
The number of probes to be multiplexed in the Flex
run. Defaults to single plex.
--barcode, -b BARCODE
Barcode(s) to demultiplex. Can be provided multiple
times. Mutually exclusive with --multiplex. Defaults
to single-plex when omitted.
--r1_length R1_LENGTH
The length of the R1 read. Can optimize the probe
mapping speed and accuracy.
--r2_length R2_LENGTH
The length of the R2 read. Can optimize the probe
mapping speed and accuracy.
--allow_indels Allow indels in the probe error correction. Note that
cell barcode correction is based on the technology
used.
--skip_constant_seq If the technology (i.e. Flex) has a constant sequence
in the probe design, do not filter reads for missing
it. This is useful for reads that are too short to
capture the full probes.
--allow_any_combination
Allow any combination of probes to be used for gapfill
--cellranger_output, -wta CELLRANGER_OUTPUT
Path to either the filtered_feature_bc_matrix.h5 or
the sample_filtered_feature_bc_matrix folder from
CellRanger. Can be specified multiple times to merge
multiple samples if multiplex (in order of provided
barcodes).
--expected_gap_length EXPECTED_GAP_LENGTH
Override the computed expected gap length. If not
provided, the gap length will attempt to be inferred
from the expected gap sequence in the probe inputs
file. This value is used to allow for more lenient
parsing when the R2 length is not enough to fully
sequence the RHS of all probes.
[--trim_probes TRIM_PROBES] [-r1 READ1] [-r2 READ2]
[--unmapped_reads UNMAPPED_READS]
[--flexible_start_mapping] [--project PROJECT] -o OUTPUT
[-c CORES] [-n N_READS_PER_BATCH] [-t THRESHOLD]
[--technology {Flex,Flex-v2,Flex-v2-R1,VisiumHD,Visium-v1,Visium-v2,Visium-v3,Visium-v4,Visium-v5,Custom}]
[--tech_def TECH_DEF] [--overwrite]
[--multiplex MULTIPLEX] [--barcode BARCODE]
[--r1_length R1_LENGTH] [--r2_length R2_LENGTH]
[--allow_indels] [--skip_constant_seq]
[--allow_any_combination]
[--cellranger_output CELLRANGER_OUTPUT]
[--expected_gap_length EXPECTED_GAP_LENGTH]
Quantify the genotypes of Gap-filling probes.
Options:
-h, --help show this help message and exit
--version, -v Show the version of the GIFTwrap pipeline.
--probes, -p PROBES Path to the generated gap-filling probe set file.
--trim_probes TRIM_PROBES
If > 0, trim the probes to the given length before
mapping. This can be useful if the probes have a
common sequence at the end that is not expected to be
sequenced. If the probe file contains expected
gapfills, this will be used to inform the trimming.
-r1, --read1 READ1 Path to the R1 file. Either the fastq/fastq.gz file,
or a file prefix to find a set of files.
-r2, --read2 READ2 Path to the R2 file. Either the fastq/fastq.gz file,
or a file prefix to find a set of files.
--unmapped_reads UNMAPPED_READS
If provided, unmapped reads are written to the file
prefix given.
--flexible_start_mapping
If set, we no longer assume that the R2 read starts
with the LHS probe and that there may be an insertion
that would need to be trimmed.
--project PROJECT The generic name for the project. Used to
automatically find R1 and R2 fastq files. Mutually
exclusive with -r1 and -r2 arguments.
-o, --output OUTPUT Name of the output directory.
-c, --cores CORES The number of cores to use. Less than 1 defaults to
the number of available cores.
-n, --n_reads_per_batch N_READS_PER_BATCH
The number of reads to process in a batch. Defaults to
10 million
-t, --threshold THRESHOLD
The maximum edit distance for fuzzy matching probes
and cell barcodes per 10bp.
--technology, -e {Flex,Flex-v2,Flex-v2-R1,VisiumHD,Visium-v1,Visium-v2,Visium-v3,Visium-v4,Visium-v5,Custom}
The technology used to generate the gap-filling
probes. Default is Flex. If 'Custom', you must provide
the --tech_def argument.
--tech_def TECH_DEF The path to the technology definition python file to
import. Must include a single class definition that
inherits from TechnologyFormatInfo.
--overwrite, -f Overwrite the output directory if it exists.
--multiplex, -m MULTIPLEX
The number of probes to be multiplexed in the Flex
run. Defaults to single plex.
--barcode, -b BARCODE
Barcode(s) to demultiplex. Can be provided multiple
times. Mutually exclusive with --multiplex. Defaults
to single-plex when omitted.
--r1_length R1_LENGTH
The length of the R1 read. Can optimize the probe
mapping speed and accuracy.
--r2_length R2_LENGTH
The length of the R2 read. Can optimize the probe
mapping speed and accuracy.
--allow_indels Allow indels in the probe error correction. Note that
cell barcode correction is based on the technology
used.
--skip_constant_seq If the technology (i.e. Flex) has a constant sequence
in the probe design, do not filter reads for missing
it. This is useful for reads that are too short to
capture the full probes.
--allow_any_combination
Allow any combination of probes to be used for gapfill
--cellranger_output, -wta CELLRANGER_OUTPUT
Path to either the filtered_feature_bc_matrix.h5 or
the sample_filtered_feature_bc_matrix folder from
CellRanger. Can be specified multiple times to merge
multiple samples if multiplex (in order of provided
barcodes).
--expected_gap_length EXPECTED_GAP_LENGTH
Override the computed expected gap length. If not
provided, the gap length will attempt to be inferred
from the expected gap sequence in the probe inputs
file. This value is used to allow for more lenient
parsing when the R2 length is not enough to fully
sequence the RHS of all probes.