[mira_talk] Re: polyA masking using mira internal routines

On Tuesday 15 February 2011 16:40:15 Michele Vidotto wrote:
> I want ask if  there is a way to force MIRA to not produce debris but
> to ensure that all sequences that are not assembled end up as
> singletons in the output file.

Hello Michele,

please do not hijack a running thread, open a new one so that readers can 
easily decide whether the thread is interesting to them or not.

That being said: since the 3.2 series, there is cross-influence between -
OUT:sssip:stsip and the parameter which defines the minimum number of reads per 
contig (-AS:mrpc). That is also noted in the manual.

If you really want singlets, you need to tell MIRA that the contigs may have 
only one read. So, if you have 454 sequences, use

  454_SETTINGS -AS:mrpc=1

(after the "--job=..." please)

Similar strategy if you have Sanger, Solexa, ...

B.

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