[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 17:13:58 +0000

On 23/02/11 16:59, Peter wrote:
I don't really expect them to when there are more well defined file
formats out there. Consider that MIRA already supports at least 3
different pair-end naming conventions, so for Tablet to try and
guess what's in the ACE file is quite tricky.

Hi, Peter.

I use the MIRA ace file because I'm still using Consed, but I now want to get a better overview of my 454 + Solexa assembly using Tablet.

I'm hoping that if there is enough demand, the Tablet team might
be persuaded to support the MIRA assembly format (MAF) directly.
This does have explicit pair information (although not as helpful as
SAM/BAM in that you have to scan the whole file to find the mate
pairs). Plus the MAF (and ACE) files can contain contig region tag
information which SAM/BAM does not support.

I had to do quite a lot of work to get a sorted and indexed BAM file from the SAM file your Python script created. After all that, Tablet told me that the "samtools" installed in Bio-Linux6 is too old :-)

It loaded it, though...

I'm happy to have any feedback on the MIRA list.

OK, brace yourself ;-)

Your script was useful, but unless I'm doing something wrong with it quite a bit of post-processing is needed to get a BAM file that Tablet can use to display mate-pairs, and all insert sizes are reported as zero...

Maybe I'll go back to trusty old Hawkeye ;-)

Thanks again for the jungle tip,

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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