giftwrap-summarize
The giftwrap-summarize command takes processed GIFT-seq data and generates a basic QC summary report and, if given, filters the data based on an already generated cellranger output. This command is useful for summarizing the results of GIFT-seq processing and ensuring that the data meets quality standards.
giftwrap-summarize --helpUsage: giftwrap-summarize [-h] [--version] --output OUTPUT [--overwrite]
[--cellranger_output CELLRANGER_OUTPUT]
[--reads_per_gapfill READS_PER_GAPFILL] [--flatten]
Generate summary statistics for counts.
Options:
-h, --help show this help message and exit
--version, -v Show the version of the GIFTwrap pipeline.
--output, -o OUTPUT Path to the output directory.
--overwrite, -f Overwrite the output files if they exist.
--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 the
counts.N.h5 files is sorted by N).
--reads_per_gapfill READS_PER_GAPFILL
The minimum number of reads supporting a gapfill to
include it in the final counts. Default is 0 (no
filtering).
--flatten Flatten the final output to a gzipped tsv file.
[--cellranger_output CELLRANGER_OUTPUT]
[--reads_per_gapfill READS_PER_GAPFILL] [--flatten]
Generate summary statistics for counts.
Options:
-h, --help show this help message and exit
--version, -v Show the version of the GIFTwrap pipeline.
--output, -o OUTPUT Path to the output directory.
--overwrite, -f Overwrite the output files if they exist.
--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 the
counts.N.h5 files is sorted by N).
--reads_per_gapfill READS_PER_GAPFILL
The minimum number of reads supporting a gapfill to
include it in the final counts. Default is 0 (no
filtering).
--flatten Flatten the final output to a gzipped tsv file.