When I use the option --report-secondary-alignments in TopHat, cuffdiff reports that there are fewer fragments mapping to some genes in the genes.count_tracking file.
Without any filtering following TopHat I would expect counts to be increased in most cases when using the -report-secondary-alignments option? Does anyone know what might be going on here?
(My ultimate aim is to remove non-unique alignments, but when I do this (using samtools view -bq 4) without first reporting secondary alignments there appears to be no change in the results, so I started exploring other options i.e. --report-secondary-alignments).