[mira_talk] Solexa paired-end reads

  • From: Tony Travis <a.travis@xxxxxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Wed, 23 Feb 2011 13:17:07 +0000

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.

This is the MIRA command-line I used:

mira -project=meta \
        -job=denovo,genome,normal,454,solexa \
        COMMON_SETTINGS -GE:not=8 -SK:nrr=50 \
        454_SETTINGS -LR:lsd=on,ft=fasta \
        SOLEXA_SETTINGS -LR:lsd=on,ft=fastq

Can you enlighten me?


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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