extract reads covering splice junctions
getJunctionReads.RdgetJunctionReads extract reads from scanBam that cover splice junctions.
Arguments
- read_info
output from
scanBamcontaining details of the aligned reads for VDJ, C and intronic regions.
Value
A data.frame containing details of reads which cover splice junctions:
- qname
read ID in the FASTQ/BAM
- CB)
cell barcode
- UB)
Unique molecule identifier (UMI)
- type
a list of mapped entities (VDJ/IGHC genes/intronic rgeions) found on the read.
Details
getJunctionReads extract reads from scanBam that cover splice junctions.
This considers only those which cover BOTH VDJ and C exons/introns, and
strange cases which cover multiple different IGHC genes.