[miso-users] Paired end reads with different read length

[Yarden Katz]

Hi Marcin,

MISO does not currently support mixed read lengths in the same BAM file.  The only way to apply MISO to these files is to separate your reads by length, and run MISO individually on fixed read length files.

If your insert length generates overlapping reads, that should not be a problem.  You just specify the mean and standard deviation of your distribution, which can be estimated using the "pe_utils.py" script.

Best, --Yarden


On Jul 10, 2012, at 9:39 AM, Marcin Piechota wrote:

> Hi,
> 
> I get stuck with a problem while trying to use MISO.
> I have paired-end data from SOLiD with different read length 50 for F3 and 35 for F5.
> RNA fragments length is about 100 +/- 30, so sometimes reads overlap.
> 
> How should I set --read-len and --paired-end parameters?
> 
> I would be gratefull for any help,
> Marcin Piechota
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