[mira_talk] Re: Solexa paired-end reads
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 23 Feb 2011 15:33:48 +0000
On 23/02/11 15:16, Peter wrote:
On Wed, Feb 23, 2011 at 1:17 PM, Tony Travis<a.travis@xxxxxxxxxx> wrote:
Hi, Bastien.
I'm assembling Solexa paired-end reads with MIRA using the default Solexa
read-naming convention, but I have no idea if MIRA is actually using the
mate-pair information. I've looked at the logs, but I can't find any
information about mate-pairs.
I have to admit that I just assumed mate-pair information is used by MIRA.
However, when I used the "tablet" viewer to examine a MIRA 'ace' file from
my Solexa paired-end assembly, it showed no mate-pairs.
Hi Tony,
Ace files don't store paired end information explicitly, so Tablet can't show
you anything.
Hi, Peter.
Well, ace files store read-names(!) and the read-naming convention
normally includes the read direction but Iain Milne just told me that
Tablet can't parse this information out of ace files at present.
I've used AMOS to convert ace files to 'bank' format for Hawkeye, which
can then find and display mate-pairs. However, now I want to use Tablet.
I therefore wrote a MIRA assembly format (MAF) to SAM
converter which should then allow you to see the pairs in Tablet (or any
other SAM/BAM viewer): https://github.com/peterjc/maf2sam
Great, I'll try that out - Thanks!
I'm happy to have any feedback on the MIRA list.
OK, brace yourself ;-)
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
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