I am trying to align paired-end data from Illumina (300bp x 2) to a draft genome. First of all I use Trimmomatic to remove adapters and bad quality ends. later I tried to map the reads; first with Bowtie2 alone and later with TopHat2 (which uses Bowtie2).

Bowtie2 alone mapped about 68% of the reads while Tophat about 40%, with which parameters is TopHat calling Bowtie that the alignment rate decrease instead of increasing? Since the reads are quite long (up to 300nuc) should I modify the --read-edit-dist and -N parameters (in this way I get more percentage of mapped reads, but I don't know if I'm getting ad alignments)?

Thank you very much