giftwrap-correct-umis
The giftwrap-correct-umis command is used to manually correct UMIs (Unique Molecular Identifiers) in GIFT-seq data. This command is typically run after the initial counting step to ensure that UMIs are accurately processed and corrected. It additionally allows for correction of PCR chimeras/artifacts.
giftwrap-correct-umis --helpUsage: giftwrap-correct-umis [-h] [--version] --output OUTPUT
[--threshold THRESHOLD] [--cores CORES]
[--n_cells_per_batch N_CELLS_PER_BATCH]
[--allow_chimeras]
Correct cell UMIs and filter out identical values.
Options:
-h, --help show this help message and exit
--version, -v Show the version of the GIFTwrap pipeline.
--output, -o OUTPUT The name of the output directory.
--threshold, -t THRESHOLD
The edit distance threshold per 10bp for fuzzy
matching. Default is 1.
--cores, -c CORES The number of cores to use. Less than 1 defaults to
the number of available cores.
--n_cells_per_batch, -n N_CELLS_PER_BATCH
The number of cells to process in a given batch.
Defaults to 1 thousand.
--allow_chimeras, -ac
Allow chimeric gapfills. If unset, umis that occur
multiple times per cell will be collapsed to the most
common probe. If set, there is no collapsing.
[--threshold THRESHOLD] [--cores CORES]
[--n_cells_per_batch N_CELLS_PER_BATCH]
[--allow_chimeras]
Correct cell UMIs and filter out identical values.
Options:
-h, --help show this help message and exit
--version, -v Show the version of the GIFTwrap pipeline.
--output, -o OUTPUT The name of the output directory.
--threshold, -t THRESHOLD
The edit distance threshold per 10bp for fuzzy
matching. Default is 1.
--cores, -c CORES The number of cores to use. Less than 1 defaults to
the number of available cores.
--n_cells_per_batch, -n N_CELLS_PER_BATCH
The number of cells to process in a given batch.
Defaults to 1 thousand.
--allow_chimeras, -ac
Allow chimeric gapfills. If unset, umis that occur
multiple times per cell will be collapsed to the most
common probe. If set, there is no collapsing.