I'm checking my tophat output data and I would like to know the rate of this multiple alignments are acceptable or not
whether is dependent this rate of multiple alignments to type of genome or not? this RNA-seqs have belonged to Human.
Reads: Input : 36238973 Mapped : 30511468 (84.2% of input) of these: 14351857 (47.0%) have multiple alignments (15253 have >20) 84.2% overall read mapping rate.
thanks in advance