[miso-users] Read trimming resulting in different read lengths

[guenter raddatz]

Dear Miso-Experts,

I have paired end Illumina data (100bp) which I have mapped with tophat.
Before mapping I routinely trim poor quality stretches from the ends of the
reads, allowing a minimum read length of 30bp. So the mapped reads have
all possible lengths between 30bp and 100bp. Can I process my mapped
data with MISO, or is there a problem regarding the parameter --read-len ?

Thanks,
Guenter