[mira_talk] Re: mid-tags

+++ Bastien Chevreux (18.02.2009 14:59):
[...]
The problem with all three possibilities above: even though a number of people have inquired previously by mail regarding this topic, I yet haven't got back any script that performs this kind of data mangling[*]. Feel free to be the first :-) 

Regards,
  Bastien
[*] I would assume that this belongs to "normal" data processing that the Roche software should perform, but until now this is not part of their software pipeline. 



The Roche software itself is writing 5' and 3' trim points into the sff
file; the 5' trim point is usually set to base position 5 (after the key
sequence 'TCAG'). The software can (sfftools, sfffile) split sff
archives by their MID sequences, which means for every MID found
there is a new sff file created with the 5' trim point shifted by
10 bases (or whatever length of MID is configured) to 3'.

I do agree with Greg that the 5' key sequences and barcodes should be
removed physically from the sequences as they are not part of the
sequence itself (in a biological sense).

just my 2p,
Sven


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