[mira_talk] Re: Mapping denovo contigs with Reference
- From: Adnan Niazi <niazi84@xxxxxxxxxxx>
- To: mira talk <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 20 May 2010 08:17:01 +0000
>
> Yes, at least partly. MIRA has a maximum read length of 20k at the moment, so
> you have to shred the contigs you got into smaller pieces (shreds, frags or
> whatever you want to call them) ... depending on what you want, this could be
> anything from 500bp to 20kbp. You can use "fasta2frags.tcl" script from the
> MIRA package for that.
How we call those shreds in parameters, i mean will they come under
SOLEXA_SETTINGS or someone else. I am interested in knowing shreds input
parameters in this case, whether they will be sanger, solexa etc.
> The only application for what you want to do would be to check for
> misassemblies or genome reorganisations (if the reference is different from
> what was sequenced). The first case would be ok, in the sewcond case I would
> not use shreds of contigs, but directly the Solexa reads. Especially if they
> are 75mers.
The sequence i am saying Reference sequence is actually consensus sequence
(unpadded fasta file) which i got after mapping solexa 75mers using MIRA3,
still need to check missassemblies?
Regards
/adnan
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