sc_correct_bam_bc: sc_correct_bam_bc
In scPipe: pipeline for single cell RNA-seq data analysis

Description Usage Arguments Value Examples

update the cell barcode tag in bam file with corrected barcode output to a new bam file. the function will be useful for methods that use the cell barcode information from bam file, such as 'Demuxlet'

1 2	sc_correct_bam_bc(inbam, outbam, bc_anno, max_mis = 1, bam_tags = list(am = "YE", ge = "GE", bc = "BC", mb = "OX"), mito = "MT", nthreads = 1)

`inbam`	input bam file. This should be the output of `sc_exon_mapping`
`outbam`	output bam file with updated cell barcode
`bc_anno`	barcode annotation, first column is cell id, second column is cell barcode sequence
`max_mis`	maximum mismatch allowed in barcode. (default: 1)
`bam_tags`	list defining BAM tags where mapping information is stored. "am": mapping status tag "ge": gene id "bc": cell barcode tag "mb": molecular barcode tag
`mito`	mitochondrial chromosome name. This should be consistant with the chromosome names in the bam file.
`nthreads`	number of threads to use. (default: 1)

no return

data_dir="celseq2_demo"
barcode_annotation_fn = system.file("extdata", "barcode_anno.csv",
    package = "scPipe")
## Not run: 
# refer to the vignettes for the complete workflow
...
sc_correct_bam_bc(file.path(data_dir, "out.map.bam"),
    file.path(data_dir, "out.map.clean.bam"),
    barcode_annotation_fn)
...

## End(Not run)