I have bam files that I have split into unmapped, uniquely mapped and multimapped bam files from HISAT2 alignment. I am trying to merge the sorted unmapped and uniquely mapped bam files with the command
samtools merge A1_merged.bam -b A1_unmapped.bam A1_unique.bam
and am getting an error
[E::hts_open_format] Failed to open file BAMT samtools merge: fail to open "BAMT": No such file or directory
the square actually has a question mark in it but that didn't copy across. Anyone have any ideas on why this error is coming up and how to fix it?