[mira_talk] Re: How to disable right end base masking for solexa data in mira.

On May 10, 2012, at 20:23 , Markiyan Samborskyy wrote:
> Is  there  a way of disabling the masking (conversion to the n) of the
> first  base in every solexa read (miseq), other then telling MIRA that
> they come from 454?

No, sorry, at least not in the 3.4 line, but this has been fixed in the 3.9 
line. I used this trick to hide comments in gap4.

> The  reads  are preprocessed by my fastq import/filter tool and have all 
> detectable
> crap removed/clipped, so only good sequence should remain.

Be careful: if you did a quality clipping, chances are that you might have cut 
too much and that this will result in lower quality assemblies (more gaps). 
What you can do: cut away all adapters you want, but leave the rest to MIRA 
(and the proposed end clipping, -CL:pec). It's doing a pretty good job as 
several people reported, also on this list.

> But  it  still  changes  the  first  base in every read to n, and sets
> quality to 0. And as a results all reads in the resulting ace file doesn't
> match  the  phd.ball  files, and the consed (v22) is complaing... (and
> doesn't show any read quality data).

Simple workaround: use gap5 :-) OK,ok, I know, probably not what you wanted to 
hear.

B.



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