I am using megablast to align my assemblies to a reference. It is extremely important for me to be able to determine if certain alignments are from the reverse strand or from the forward strand. Using tabular output, there is an output criteria "sstrand" which gives the subject strand of the alignment. However, this sstrand option only gives "plus" output unless megablast is run with the "-strand both" option. On the surface, this makes sense - except that the "strand" option's description refers to the query strand - "Query strand(s) to search against database/subject. Choice of both, minus, or plus."
In theory (at least to my knowledge), the following should give equivalent results: 1) Aligning both reverse complement and forward strand in the subject to the forward strand in the query 2) Aligning the forward strand in the subject to both the reverse complement and forward strand in the query
So my question boils down to this:
Does Megablast align both the positive and reverse complement strand of the subject strand, no matter the setting for "strand," or is there a typo in the documentation?
What happens if the query is the one with the "minus" match? There is no corresponding "qstrand" option in Megablast's output - how do I find out the strandedness of the query?
It is extremely perplexing that the "sstrand" output only gives you "minus" as an output when you allow "strand both", e.g. you allow the query strand to be both plus and minus. The "strand both" option does not explicitly say anything about allowing both strand orientations in the subject.