giftwrap-correct-gapfill
The giftwrap-correct-gapfill command is used to manually correct gapfill sequences in GIFT-seq data. This command is typically run after the initial counting and UMI correction steps to ensure that gapfill sequences are accurately processed.
giftwrap-correct-gapfill --helpUsage: giftwrap-correct-gapfill [-h] [--version] --output OUTPUT
[--cores CORES]
[--n_groups_per_batch N_GROUPS_PER_BATCH]
Correct and deduplicate gap fills.
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.
--cores, -c CORES The number of cores to use. Less than 1 defaults to
the number of available cores.
--n_groups_per_batch, -n N_GROUPS_PER_BATCH
The number of (barcode, umi, name) groups to process
in a given batch. Defaults to 100 thousand.
[--cores CORES]
[--n_groups_per_batch N_GROUPS_PER_BATCH]
Correct and deduplicate gap fills.
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.
--cores, -c CORES The number of cores to use. Less than 1 defaults to
the number of available cores.
--n_groups_per_batch, -n N_GROUPS_PER_BATCH
The number of (barcode, umi, name) groups to process
in a given batch. Defaults to 100 thousand.