I noticed that the BAM files contain unmapped reads (at least it looks like it from the size and total read vs mapped reads stats). I think it just takes up space to store unmapped reads, they don't really have a use. You can suppress them by filtering with -F 4 when writing the bam file.
I noticed that the BAM files contain unmapped reads (at least it looks like it from the size and total read vs mapped reads stats). I think it just takes up space to store unmapped reads, they don't really have a use. You can suppress them by filtering with -F 4 when writing the bam file.