[miso-users] Strand filtering when running MISO

[Yarden Katz]

Hi David,

There's no such flag for now, but I could add an option to the MISO configuration file to tell it to discard all FR/RF reads and only keep FF or RR reads.  I've never encountered such a dataset before so did not think to add it.  

Best, --Yarden




On Oct 8, 2012, at 11:45 AM, David Wood wrote:

> Hello MISO users,
> 
> My BAM file contains paired reads in the orientation FF or RR (eg both 
> reads are on the same strand).  Is it possible to configure MISO to keep 
> these reads and discard those in orientation FR or RF? Currently it is 
> discarding all the properly paired reads.
> 
> Regards,
> David
> 
> 
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