sc_count_aligned_bam {scPipe} | R Documentation |
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)
inbam |
input aligned bam file |
outbam |
output bam filename |
annofn |
single string or vector of gff3 annotation filenames |
bam_tags |
list defining BAM tags where mapping information is stored.
|
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. |
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. |
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)