[mira_talk] Re: mid-tags

On Wednesday 18 February 2009 Gregory Harhay wrote:
> I've sent Bastien a revamped bin_fasta_on_mid_primers.pl. The script bins
> the reads according to their mid primers and removes them as in in case 1
> below. 
> [...]

Yikes, I totally forgot the existence of your binning script, sorry Greg. I'm 
in the midst of shifting to a new computer at home and should have transferred 
the MIRA archives before answering the mail ... would this count as excuse?

The updated script will appear sometime tomorrow on the web site.

> My rational for doing this is that these mid primers are not
> biologically entities and I don't want the assembler to use them or the
> space they occupy in "assembly space". I assemble with -LR:mxti=no so that
> mira doesn't use the XML file.

That approach is totally valid. However, the reason why I prefer the "soft" 
clip-away- with-ancillary-data approach is simple: there's always the 
possibility of human error at any step in the processing pipeline. Then 
there's still the possibility to check in the "hidden" data whether everything 
was done correctly.

I remember a project (done with Sanger sequencing and specially designed 
vectors) where during pre-processing every non-relevant data was clipped away 
... but someone mistakenly mixed in a wrong file with the wrong species 
sequences and I had quite some fun in finding out what had happened when there 
were "strange results" in the data set.

Since then, I try to always keep this kind of extra information.

Regards,
  Bastien


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