[mira_talk] Re: After Scaffolding

  • From: Davide Sassera <davide.sassera@xxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 07 Sep 2009 21:08:30 +0200

Dear all,
thanks to Gregory and Giuseppe I managed to install Bambus, so know we know it works on Ubuntu 8.04 also.

I made it run and I get one scaffold of the expected size, it's great.

But, now, as Giuseppe pointed out, how we get the best from the output?

I can generate a fasta file of the scaffold, as Gregory explained, but that has two problems IMHO:
it has many stretches of Ns and
is not possible to check the reads and the matches.
I do not feel comfortable to use it "as it is", I would like to check it in gap4 or any other editor, to see if the joins are correct.

What do you guys do? you take the Bambus output as "right" as it is or you have a method to check the quality and possibly modify the scaffold?

thank you all


iuseppe D'Auria wrote:
Dear all,
Now that Bambus is working and I obtained the outfiles with the order of
contigs, there is a way to order and orient automatically my contigs in
the .caf file in order to open my GAP4 and see the genome in a
fashionable ordered and oriented way?

I am think to something like

myproject.caf --> myproject_ordered.caf --> caf2gap -->Gap4

Thank you in advance


Davide Sassera
Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale, Igiene e Sanità Pubblica Veterinaria Facoltà di Veterinaria
Università degli Studi di Milano
Via Celoria 10, 20133, Milano, ITALY
Tel: +39 0250318094
Fax: +39 0250318095

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