[mira_talk] Re: Solexa paired-end reads
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: "peter@xxxxxxxxxxxxxxxxxxxxx" <peter@xxxxxxxxxxxxxxxxxxxxx>
- Date: Thu, 24 Feb 2011 11:46:54 +0000
On 24/02/11 11:14, Peter wrote:
On Thu, Feb 24, 2011 at 10:23 AM, Tony Travis<a.travis@xxxxxxxxxx> wrote:
... you can estimate insert sizes from mate-pairs placed in the same
contig, which is how Consed does it.
That is what I was thinking of doing in the maf2sam script (complicated
by paired end vs mate pairs etc). For the assemblies I've been using
this on however, my paired end reads are all Sanger reads where the
distribution of fragment lengths is expected to vary widely, and I was
happy to just look at the read placement in the assembly.
Hmm. I wonder if Tablet could show the inferred fragment size (insert
size) when the two reads are on the same fragment and the SAM/BAM
field is not populated (i.e. left as zero).
Hi, Peter.
We use Hawkeye to look for misassemblies, where mate-pairs are in AMOS
nomenclature 'unhappy' (i.e. stretched or compressed in comparison to
the expected insert length). It would be very useful to have a similar
function in Tablet, and I've already mentioned comparison with Hawkeye
to Iain Milne. I think Tablet is getting more useful as it develops, but
Hawkeye is popular for a good reason: Detection of misassemblies.
The problem with Hawkeye is that it is difficult to install and run.
That, in my opinion, is a major advantage of Tablet over Hawkeye but
without mis-assembly metrics, Tablet is not as useful for my work.
Despite this, I'm now starting to use Tablet because it's good :-)
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
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
