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]
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).
[--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]
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).