tophat2 aligment ratio reduced when increase insert size

Question

[52Teth]

Now I have two set of HiSeq pair end equencing data for the same sample with different insert size(196 and 225). The I use tophat2 to align the reads to the genome seperately, the tophat2 parameter (--read-mismatches 2, --read-edit-dist 2, --max-intron-length 5000000, --library-type fr-unstranded, --mate-inner-dist 40) is same. But the overall read mapping rate is different(insert size 196: 90%,insert size 196: 80% ). What's the reason causes this different? What can I do for this (such as change the tophat2 parameter)?

Thanks a lot for any advice.

[Fabio Marroni]

First of all you should see which reads you are not aligning. Maybe they are contaminants? Or low quality reads? Out of curiosity, what is the read length?