I am currently using TopHat2 to map RNA-seq runs. I think there have been some changes pertaining the -g option. Does anyone know how it works now?
I used to think that setting -g would look for n alignments for a given read, report them [if top-scoring] and discard those reads that had more than g [top scoring] alignments.
Now, the description sounds more like if there are more than g top scoring alignments for a read (assuming report-secondary-alignmennts is not on), it will choose g at random, or simply the top alignments found if they did not reach g. There does not seem to be a discarding of reads if they surpass g. However, there is an option in the help message, not in the manual, that is called --suppress-hits. I suspect this might be able to turn on the discarding of reads that exceed g alignments. Is this true?
And finally, if one sets bowtie options -k and -M (does this still exist?), do those pass on to TopHat, and do they precede over -g?
Thanks a lot,
-g/--max-multihits <int> [ default: 20 ] --suppress-hits -x/--transcriptome-max-hits <int> [ default: 60 ]