sc_correct_bam_bc {scPipe} | R Documentation |
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'
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
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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.
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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)