Mapping rate decreases using Tophat1.2.0 from 1.1.4

[zun]

hi,everyone

I updated tophat from 1.1.4 to 1.2.0,newest version recently.
Then I run tophat1.2.0 giving the same paired-end reads, but the mapping rate decreased to 22% from 37%(using tophat1.1.4) .

Is this because that 1.2.0 has become able to support Indels?
But this Indel-detection is disable as default
(it is needed to give '--allow-indels' option to enable this function,but i didin't..)
Actually tophat1.2.0 output insertions.bed and deletions.bed which are both empty. With --allow-indels option, however,these files were not empty(59K,89K).


Would somebody please explain this result for me?
Thanks in advance.

#I'm not good at English.
#so if my English make you feel bad, I'm so sorry.

[zun]

I found out the cause of above.

In tophat.py, one bowtie option has been changed
from -v to -n.
These options are mutual exclusive and the usage is described in Bowtie Manual.

I rewrote tophat.py to change -v to -n, then recomplied and run tophat against the same Read.
I got the same mapping rate as well as that of tophat1.1.4.

This option change seems to be done by daehwan, is it right?
Are there any altenative options to use -n in tophat1.2.0?

I also want to know the other ways to raise mapping rate.
My mapping rate is 37%. I think it is low..but is it usual??