I'm trying to map Illumina PE RNA-Seq data originated from one fish genus to the genome of another related genus of the same family with tophat2 software.
I started with almost default settings of tophat2 (excepting
-r flag). Then i've added
--mate-std-dev 4000 --read-edit-dist 20 to my command line, but mapping statistics is still bad.
Left reads: Input : 14811423 Mapped : 7078897 (47.8% of input) of these: 4273616 (60.4%) have multiple alignments (1521255 have >20) Right reads: Input : 14811423 Mapped : 6753768 (45.6% of input) of these: 4051398 (60.0%) have multiple alignments (1521195 have >20) 46.7% overall read mapping rate. Aligned pairs: 5026382 of these: 3371900 (67.1%) have multiple alignments 1614729 (32.1%) are discordant alignments 23.0% concordant pair alignment rate.
My questions are: Which tophat settings i have to try in my case? Which program for RNA-Seq reads mapping would be better to test besides tophat2?