[mira_talk] Re: fosmid assembly using mira
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 23 Dec 2009 12:59:15 +0100
On Mittwoch 23 Dezember 2009 Rohit Ghai wrote:
> thanks a lot for the new links. The usage is clear in the manual. I am
> currently working with MIRA V3rc1 (aka 2.9.48). so the ssaha2 is already
> being used in this version or do I have to install the one you have
> suggested ?
Take the last one, it's not yet present in rc1.
> Regardless of your comment that the paired-end section would not help, it
> did help a bit in that I realised that I needed to have qual and traceinfo
> files for my sanger data, which is essentially the ends of the fosmids we
> sequenced. I have only fasta files (no qual etc) ,can I use dummy qual
> files ? ( say with a constant quality score of say 40).
If none of your Sanger files has qualities, you do not need to generate fake
ones.
Instead, turn of "wants quality file", set the default quality for Sanger
settings to any value you like.
SANGER_SETTINGS -LR:wqf=no -AS:bdq=40
> I hope the format is alright.
If MIRA reads it, then it should be ok.
B.
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