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

[Yarden Katz]

Dear Guenter,

At the moment MISO only supports fixed read lengths -- so all reads must have the same read length, including both mates in each paired-end read.  I recommend trimming the reads to the shortest fixed length that you find to be of high quality, mapping the trimmed reads this way with Tophat, and giving MISO the fixed read length in "--read-len".

Best, --Yarden




On Dec 3, 2012, at 4:14 PM, guenter raddatz wrote:

> 
> 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
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