Can Smash++ take reverse complement into account?

[Sean-McGinty]

I was using Smash++ to identify rearrangements between a reference and a target genome. Unknown to me, the target sequence was actually on the - strand in the 3'-5' direction. It was telling me my entire sequence was inverted so I tried the reverse complement and got the anticipated result. Would there be any way that Smash++ could take reverse complement into account?

[pratas]

Dear,

The reverse complement of a reverse complement is the direct detected region. I guess the way you provided the reverse complement before running smash++ works fine. If you are looking to have a tool to do this automatically before running smash, please see GTO (https://cobilab.github.io/gto). For example with: gto_fasta_to_seq < a.fa | gto_reverse | gto_genomic_complement | gto_fasta_from_seq -n "Reverse complemented" > reverse_a.fa

Best regards, Diogo