[mira_talk] Re: mid-tags

No offence taken. Looks like Sven's got a much better process for dealing
with the MID primers. Thanks Sven!

Greg


On 2/18/09 6:27 PM, "Bastien Chevreux" <bach@xxxxxxxxxxxx> wrote:

> 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
> 

Gregory P. Harhay, PhD
Computational Biologist
Animal Health Research Unit
USDA-ARS-Roman L. Hruska  U.S. Meat Animal Research Center
Clay Center, NE 68933
v - 402.762.4250




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