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Scan reads mapped to a given genomic range

scanBam.Rd

scanBam looks for reads in a BAM file which are mapped to a genomic range given by the parameter gRange.

Usage

scanBam(bam, gRange, cellBarcodeTag = "CB", umiTag = "UB", paired = FALSE)

Arguments

bam

filepath to the BAM file to read

gRange

GenomicRanges::GRanges object specifying the genomic range to scan. See Examples.

cellBarcodeTag

Name of tag holding information about cell barcode. The code expects and extracts this tag from each line in the BAM alignments. Set as NULL or NA if no such information is available in the BAM file. (Default: "CB")

umiTag

Name of tag holding information about molecule barcode. The code expects and extracts this tag from each line in the BAM alignments. Set as NULL or NA if no such information is available in the BAM file. (Default: "UB")

paired

Are the sequencing reads paired-end? (Default: FALSE)

Value

A data.frame:

qname

read ID in the FASTQ/BAM

rname

chromosome

pos

genomic position

cigar

CIGAR string indicating the result of aligning the sequencing read to the nominated position in the genome. See the SAM format specification document linked above in the Description for details

flag

the FLAG field in the SAM file. Indication of the nature of the alignment. See the SAM specification linked above in the Description for more details.

cellBarcodeTag (Default: "CB")

cell barcode

umiTag (Default: "UB")

Unique molecule identifier (UMI)

The scanning of the BAM file by default removes secondary alignments, duplicates and reverse complement alignments.

Details

The function looks for BAM alignments which are mapped to the genomic range given by the parameter gRange. All alignments which *span across* gRange but do not have bases which reside within the range will be ignored (e.g. a spliced read spans across a given range but will not have any bases which map to the spliced range). The function expects [standard BAM/SAM format specification](https://samtools.github.io/hts-specs/SAMv1.pdf) plus additional tags indicating the associated cell and molecule barcodes. Set cellBarcodeTag and/or umiTag as NULL or NA if these tags are absent from the given BAM file.