[miso-users] Strand filtering when running MISO

[David Wood]

Thanks Yarden,

It's a BAM file I created myself and for other reasons flipped the 
strand flag on R2 reads - the library is created FR/RF.  It may be 
useful to make a flag but for now I think I'll just flip all the R2 
reads back so I can use the software.  Only make the change if you think 
it will be more broadly useful.

Regards,
David

On 8/10/12 7:35 PM, Yarden Katz wrote:
> 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
>>
>>
>> _______________________________________________
>> miso-users mailing list
>> miso-users at mit.edu
>> http://mailman.mit.edu/mailman/listinfo/miso-users

-- 

David Wood
PhD Student

Queensland Centre for Medical Genomics

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