cassiopeia.pp.error_correct_cellbcs_to_whitelist#
- cassiopeia.pp.error_correct_cellbcs_to_whitelist(bam_fp, whitelist, output_directory, n_threads=1)[source]#
Error-correct cell barcodes in the input BAM.
The barcode correction procedure used in Cell Ranger by 10X Genomics is used. https://kb.10xgenomics.com/hc/en-us/articles/115003822406-How-does-Cell-Ranger-correct-barcode-sequencing-errors This function can either take a list of whitelisted barcodes or a plaintext file containing these barcodes.
- Parameters:
- bam_fp
str
Input BAM filepath containing raw barcodes
- whitelist
Union
[str
,List
[str
]] May be either a single path to a plaintext file containing the barcode whitelist, one barcode per line, or a list of barcodes.
- output_directory
str
The output directory where the corrected BAM will be written to. This directory must exist prior to calling this function.
- n_threads
int
(default:1
) Number of threads to use. Defaults to 1.
- bam_fp
- Return type:
- Returns:
Path to corrected BAM