[mira_talk] Re: mira 3.0.1 crashes in mapping mode
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 30 Mar 2010 15:01:50 +0100
On 30/03/10 10:40, Tony Travis wrote:
[...]
I suppose it could. I never found the time to analyse the format of these
things though ... there are quite a number of other things I need to tackle
first. I spoiled: as I use gap4 with CAF (and caf2gap), I don't have any of
these problems :-)
In fact, a phd.ball is just a concatenation of phd files in a single
file and I created a phd.ball for the 454 fasta+quals using the attached
perl script "qual2ball". I've tried caf2gap, but the 32-bit version runs
out of memory on our 3.7Mbp genome and the 64-bit version segfaults.
[...]
Hello, Bastien.
Here's a way to create a consistent MIRA phd.ball for Consed:
Run MIRA on project "all" to create:
all_assembly/all_d_results/all_out.ace
all_assembly/all_d_results/all_out.fasta.caf
Extract the reads and qual's in FASTA format:
cd all_assembly/all_d_results/
caf2phrap -caf all_out.caf -fasta all_out.fasta
Use my script to create a phd.ball from the FASTA files:
qual2ball all_out.fasta >phd.ball
The phd.ball created should now contain base-calls and quality scores
that are consistent with the MIRA ace/caf file:
mkdir ../phd_dir # needed in order for Consed to start up
consed -allowTimestampMismatch -ace all_out.ace # reads phd.ball
Works perfectly - Goodbye gap5 ;-)
Bye,
Tony.
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis@xxxxxxxxxx, http://bioinformatics.rri.sari.ac.uk/~ajt
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