I am aligning CDS sequences I downloaded from Ensembl to some draft assemblies someone has published. I used LAST to align then, and it appears to have worked, see example here:
What I can't figure out is that for most of the query CDS's ("O_niloticus" lines in the example), some of the transcript aligns to the + strand of the assembly, and others to - strand. This seems to be the case only when a single CDS aligns to multiple different contigs (e.g. L_fuelleborni.EQ177488 and L_fuelleborni.ABPK01036261.1 are different contigs...I think), i.e. all of the CDS alignments within a contig seem to be on the same strand.
So, my question is: why would this be the case? These are fairly closely related species, so I don't think chimerism/rearrangement is plausible (again, its nearly every CDS). Is it possible the orientation of the contigs assembly is not yet determined? If that's the case can I just reverse compliment the - strand alignments and tack them (with spaces) together with the + strand bit? The end application is a FASTA for each query CDS containing all the matching sequences from a number of other species (for PAML).
Any insight would be greatly appreciated!
