[mira_talk] Re: Mappging to Reference

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sat, 12 Jun 2010 22:01:28 +0200

On Freitag 11 Juni 2010 Saulo Alves wrote:
> Sorry if i didn't make myself clear.
> events stands for all the tags mira add's to the sequencing. Gaps,
> SNPs, repeats.
> I have tried the AO process but, after placing the gaps, there are
> still discrepancies.
> for one chromossome my FASTA reference has 1.462.416 bp. the "PADDED"
> (w/ gaps) generated sequence has 1.462.514 bp and the "UNPADDED"
> sequence has 1.462.431 bp.
> There's this difference (+17) between the original and unpadded which
> i cant explain neither map back. If i want to know where in the
> reference sequence a SNP was found, i'm not able with a 17bp
> discrepancy and, for other chromossome, this difference get's even
> bigger.

Hmm ... have a look at the TCS file, column 2 & 3 with the padded pos and 
unpadded pos. Would that help?


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