Hi! I'm trying to blast a sequence where I have a TSS signal (e.g. using CapSeq) that comes from the minus strand, against a chosen genome. I already have the reverse compliment of the sequence i.e. the reverse compliment of the position of the genome, so I'm trying to force BLASTN to only use the minus strand of the chosen subject. Sadly I only found the command -strand, which takes the rev. compliment of the query and not the subject.
Did I miss the parameter in the documentation or how do you do this?
Thanks in advance!