Unclear Bowtie2 unaligned read filenames

Hi all,

When using the write unaligned reads (in fastq format) to separate file(s) option in the Bowtie2 tool (triggering the --un-conc parameter) on a paired-end library, I get two unaligned read output files: unaligned reads L and unaligned reads R. I assume that these separate files are generated to distinguish which file contains the unaligned reads from the R1 and R2 input files but can anyone clarify which file (L or R) refers to which input file (R1 and R2)?

Thanks!

minor admin reformat for clarity

1 Like

Hi @Jroels

Unmapped L reads are from the R1 input (first input on the tool form)
Unmapped R reads are from the R2 input (second input on the tool form)

The read names can confirm this.

Thanks!