hi,there is a question about tophat alignment summary,would you please answer for me ,thank you very much ！ Left reads: Input : 31687844 Mapped : 30305735 (95.6% of input) of these: 5499207 (18.1%) have multiple alignments (1287284 have >20) Right reads: Input : 31687844 Mapped : 30305735 (95.6% of input) of these: 5499207 (18.1%) have multiple alignments (1287284 have >20) 95.6% overall read mapping rate.
Aligned pairs: 30305735 of these: 5499207 (18.1%) have multiple alignments 30305218 (100.0%) are discordant alignments 0.0% concordant pair alignment rate.
so,other than this sample's concordant pair alignment rate is 0.0%,other sample's are all up to 85%,is it normal?if not,what should i do? thank you!
Did you swap the files for read #1 and read #2? That's what it looks like.