[mira_talk] Re: Illumina/Solexa sequence coverage.
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 15 Sep 2011 12:52:05 -0400
On 2011-09-14, at 2:59 PM, Bastien Chevreux wrote:
> On Sep 13, 2011, at 23:27 , John Nash wrote:
>> I really do not know. These are genuine PCR-generated reads assembled back
>> in. Can I re-add them back to an assembly (after first searching to make
>> sure that they are not hidden in a contig somewhere)?
>
> You could try to map them, yes.
>
>> I guess that I am asking what the command line parameters are to take a CAF
>> file from a hybrid assembly and then use it as input for a mapping assembly
>> against a reference genome. Or should I dump the contigs as fastq files and
>> use those.
>
> What you're looking for is
> -SB:bft=caf
>
> Also have a look at the othe -SB parameters ... you especially want to assign
> a strain to the CAF sequences and another one to the sequences of your other
> bug.
Sorry, I should have been more explicit...
Since the CAF file is a mixture of data from a hybrid assembly, do I call it
sanger, 454 or solexa (or all 3) when passing the
"--project=mapping,genome,accurate,xxx "parameters to mira
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