[mira_talk] Re: beginner q on hybrid assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 3 Sep 2009 21:27:39 +0200
On Donnerstag 03 September 2009 Sheri Simmons wrote:
> What is the best way to tell MIRA which data is
> which, and is it preferable to use phd files rather than coupled
> fasta/qual files?
Hello Sheri,
you can have one input file per sequencing technology, i.e., you can have one
phdball for the Sanger data and a FASTA/FASTA quality combo for the 454 files.
Or a FASTA/FASTA qual for Sanger and another FASTA/FASTA qual for 454.
Note: I hope the PHD reading routine works, it's been literally ages it was
used actively. It might be therefore preferable to use FASTA/FASTA qual files
as input.
> Is there a particular header format I should be
> using in the fasta file? (e.g. 454's gsAssembler has headers as
No, just standard format, MIRA does not read more than the read name and the
sequence. When using paired-end (templates), the read names however should
conform to given conventions. More on that in the documentation for the read
naming scheme paramater -LR:rns.
> And how do I indicate the presence of multiple input files on the command
> line?
As I wrote: only one input file/type per sequencing technology. Can you please
read the section "A Sanger / 454 hybrid assembly walkthrough" of the help file
dealing with 454 data? This should point you at how it's done (and if not,
don't hesitate to ask :-)
Regards,
Bastien
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