I am running an alignment of single-end reads, which are trimmed 20bp sequences that need to be aligned to my indexes of 20bp gRNAs.
I am trying to understand which bowtie2 parameters would be best for me, and came across the --norc parameter. I read the manual, but am still having trouble understanding whether I should be using this parameter or not. Can someone please describe its purpose in more understandable terms? And whether it is suggested to use it?
From the manual:
If --nofw is specified, bowtie will not attempt to align against the forward reference strand. If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand. For paired-end reads using --fr or --rf modes, --nofw and --norc apply to the forward and reverse-complement pair orientations. I.e. specifying --nofw and --fr will only find reads in the R/F orientation where mate 2 occurs upstream of mate 1 with respect to the forward reference strand.
Thank you so much.