Hi all, I got confused about minor isoform filtering when I re-read tophat paper. "The number of alignments crossing the junction is divided by the coverage of the more deeply covered side to obtain an estimate of the minor isoform frequency. If TopHat estimates that the splice junction occurs at 15% of the depth of coverage of the exons flanking it, the junction is not reported."
So, according to above statement, the junction will be excluded if it is below 15% of the depth of coverage of the exons flanking it. But what exactly is "the depth of coverage"? It's the depth of major isoform? or of minor isoform? or of average of both? As I know, usually the coverage of junctions are lower than exons, so I prefer it is 15% of minor isoform. Any comment? Did anyone manipulate this option ("-F/--min-isoform-fraction") before? I know it has been deprecated in the latest version of tophat. Any advice? Thanks, Mark