Dear all,

My goal is to extract from all reads (mapped and unmapped) a part of a sequence that aligns to a specific area in the genome.

I can do this by using this excellent command from Genomic Alignments.

please find the file in here https://1drv.ms/u/s!ArOzUuixE-mggfxdOGO9Hvpp90-qTA?e=ExC5hI

stack <- stackStringsFromBam("alignment.sorted.bam", 
                             param=GRanges("Reference_barcodes:54-78"))

stack

One sequence in the bam file is considered unmapped, but I see it maps well in the designated [54-78]. How can I retrieve the unmapped sequences from the bam file?