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

Description Usage Arguments Value Examples

Wrapper to run sc_exon_mapping, sc_demultiplex and sc_gene_counting with a single command

sc_count_aligned_bam(inbam, outbam, annofn, bam_tags = list(am = "YE", ge =
  "GE", bc = "BC", mb = "OX"), bc_len = 8, UMI_len = 6, stnd = TRUE,
  fix_chr = FALSE, outdir, bc_anno, max_mis = 1, mito = "MT",
  has_UMI = TRUE, UMI_cor = 1, gene_fl = FALSE, keep_mapped_bam = TRUE,
  nthreads = 1)

`inbam`	input aligned bam file. can have multiple files as input
`outbam`	output bam filename
`annofn`	single string or vector of gff3 annotation filenames, data.frame in SAF format or GRanges object containing complete gene_id metadata column.
`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
`bc_len`	total barcode length
`UMI_len`	UMI length
`stnd`	TRUE to perform strand specific mapping. (default: TRUE)
`fix_chr`	TRUE to add 'chr' to chromosome names, MT to chrM. (default: FALSE)
`outdir`	output folder
`bc_anno`	barcode annotation, first column is cell id, second column is cell barcode sequence
`max_mis`	maximum mismatch allowed in barcode. (default: 1)
`mito`	mitochondrial chromosome name. This should be consistant with the chromosome names in the bam file.
`has_UMI`	whether the protocol contains UMI (default: TRUE)
`UMI_cor`	correct UMI sequencing error: 0 means no correction, 1 means simple correction and merge UMI with distance 1. 2 means merge on both UMI alignment position match.
`gene_fl`	whether to remove low abundance genes. A gene is considered to have low abundance if only one copy of one UMI is associated with it.
`keep_mapped_bam`	TRUE if feature mapped bam file should be retained.
`nthreads`	number of threads to use. (default: 1)

no return

## Not run: 
sc_count_aligned_bam(
  inbam = "aligned.bam",
  outbam = "mapped.bam",
  annofn = c("MusMusculus-GRCm38p4-UCSC.gff3", "ERCC92_anno.gff3"),
  outdir = "output",
  bc_anno = "barcodes.csv"
)

## End(Not run)