Hello. I'm trying to map paired-end reads on reference scaffold using tophat2. But the percentage if mapped reads is almost 0%
Left reads: Input: 9526882
Mapped: 224 ( 0.0% of input)
of these: 22 ( 9.8%) have multiple alignments (0 have >20)
Right reads: Input: 9526882
Mapped: 230 ( 0.0% of input)
of these: 18 ( 7.8%) have multiple alignments (0 have >20)
0.0% overall read mapping rate.
Aligned pairs: 111 of these: 5 ( 4.5%) have multiple alignments
0.0% concordant pair alignment rate.
I've tried to change tophat2 options (like intron length and inner distance) and to map unmapped reads, but the result is always the same. Any suggestions are appreciated. Thanks.