[mira_talk] Re: Fwd: EST+SNP search
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 30 Mar 2010 20:28:37 +0200
On Dienstag 30 März 2010 Stephen LeGrande wrote:
> I would like to make assemblies and SNP searches from 454 EST datay and
> visualize the results in Gap4.
> However, after runnig miraSearchESTSNPs from the command line with the
>
> -OUT:output_results_gap4da=yes
>
> option, no Gap4 database will be built.
> I cannot make html output either.
> Can anybody help me ?
"Protect the innocent!" is one of the primary concerns of MIRA. In one case it
tries to protect your harddisk (and you) from creating directories with
possibly millions of files (which a gap4 direct assembly directory would need
for some 454 sets) and bring the system to an almost grinding halt. In the
other case it tries to protect your harddisk and browser from getting
submerged with HTML files the size of several gigabytes (which also can happen
with 454 data).
Now, to work with gap4 you don't need the gap4da output. Take the CAF file
from MIRA and use "caf2gap" from the Sanger Centre:
caf2gap -project somename -ace MIRA_OUTPUT.ACE
and you have a nice gap4 database.
On the other hand, if you really, really want to, you can still get the output
formats you want by using the "convert_project" tool from the MIRA package and
convert the MAF (or CAF) output of MIRA to any other supported output:
e.g.
convert_project -f maf -t gap4da MIRA_OUTPUT.MAF GAP4DIRNAME
convert_project -f caf -t html MIRA_OUTPUT.MAF HTMLNAME
Beware when doing that on data sets with hundreds of thousands of reads or
more, you have been warned :-)
Regards,
Bastien
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