[mira_talk] Re: quality clipping
- From: Adnan Niazi <niazi84@xxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 12 Apr 2010 21:34:58 +0000
Thank you very much for your quick response. I really appreciate that from
heart.
> > I am new to MIRA. I have illumina 75bp paired end data (GA-II) which i want
> > to assemble against my reference sequence.
>
> EST or genome data?
It's Genome Data of bacteria (mulitiplexed illumina paired end data)
>
> > I want to know about quality clipping option in MIRA. Should i use qc
> > option for my data as i want to
> > be very strict on data preprocessing of my assembly project.
>
> Do you know the Solexa quality metrics good enough to be a reliable judge on
> what's good and what not? I don't, and quite a few others also seem to have
> problems as every quality clipped data set I've seen so far was pretty much
> overclipped.
Well cant say about solexa quality reliability. But what i got from your
statement was that I shouldn't clip my data. If yes then can you share any
reference for reading which explains this idea because many review papers are
in strong favour of quality clipping/trimming.
> > Or proposed end clipping is enough.
>
> PEC works well only for data which is at least moderately well covered, say
> 5x
> for Sanger, 8x for Illumina. Areas covered below that (as in rare
> transcripts)
> may get clipped more harshly or even completely disappear (at 1x or 2x
> coverage) with PEC.
At what stage does PEC come in action? From well covered it seems that it works
during contig making.
> > What if i use both QC and PEC option? Should i
> > also use CPAT as well to look for poly A/T tails sequences in my data. I
> > am not sure about it.
>
> The Solexa routines already include a pretty harsh filter to throw out
> sequences with too much A/T, simply because they're very likely to be
> undetected junk from the sequencing. One of the problems of Solexa data.
Didnt get that :( Do you mean solexa is already filtered for A/T?
Regards,
Adnan
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