giftwrap-collect
The giftwrap-collect command is used to manually collect GIFT-seq data after processing, allowing for further analysis and quality control. This command is typically run after all steps of the GIFT-seq pipeline have been completed, including counting, correcting UMIs, and gapfill sequences.
giftwrap-collect --helpUsage: giftwrap-collect [-h] [--version] --output OUTPUT [--cores CORES]
[--multiplex] [--overwrite] [--flatten]
[--max_pcr_thresholds MAX_PCR_THRESHOLDS]
Collect counts into a single h5 file. Or multiple if the run was detected to
be multiplexed.
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 maximum number of cores to use.
--multiplex, -m Hint to the program that the run should be expected to
be multiplexed.
--overwrite, -f Overwrite the output files if they exist.
--flatten Flatten the final output to a gzipped tsv file.
--max_pcr_thresholds MAX_PCR_THRESHOLDS
If greater than 1, the parsed object will then have a
new layer field 'X_pcr{n}' for n in 1 to the maximum
number of PCR duplicates observed in the data. This
will increase the size of the output file, but allow
for more flexible downstream filtering.
[--multiplex] [--overwrite] [--flatten]
[--max_pcr_thresholds MAX_PCR_THRESHOLDS]
Collect counts into a single h5 file. Or multiple if the run was detected to
be multiplexed.
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 maximum number of cores to use.
--multiplex, -m Hint to the program that the run should be expected to
be multiplexed.
--overwrite, -f Overwrite the output files if they exist.
--flatten Flatten the final output to a gzipped tsv file.
--max_pcr_thresholds MAX_PCR_THRESHOLDS
If greater than 1, the parsed object will then have a
new layer field 'X_pcr{n}' for n in 1 to the maximum
number of PCR duplicates observed in the data. This
will increase the size of the output file, but allow
for more flexible downstream filtering.