[mira_talk] Re: After Scaffolding
- From: Gregory Harhay <gregory.harhay@xxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 09 Sep 2009 16:19:22 -0500
Hi Davide, Davide et al.
Sorry about my tardy response, there just aren't enough hours in the day.
The scaffolds produced by BAMBUS are just a starting point. As Bastien has
suggested, mapping reads, contigs or other genomes may give you some insight
as to the "robustness" of the build. Quite frankly, I have been handing off
the procedures to use BAMBUS and MIRA to biologist for them to analyze the
results, using some flavor of the aforementioned mapping process. But I
agree, that isn't very satisfactory. I haven't actually tried to perform the
steps suggested in the next paragraph, so take what I say with a grain of
salt. I won't be able to wrestle with these next steps for at least a month
or two.
I suggest that you look at the Hawkeye Assembly Viewer (it reportedly also
is a scaffold viewer)
http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye
as an alternatives to gap4. Here's why. It appears to use
BAMBUS and ACE files as input to produce files viewable in Hawkeye.
http://sourceforge.net/apps/mediawiki/amos/index.php?title=ToAmos
Hawkeye appears to be powerful, although I haven't used it yet. I would be
very interested if anyone got the above pipeline to work to view MIRA
assemblies/scaffolds. It is likely that others would too. Please get back to
the list if you get this to work.
Regards,
Greg
On 9/7/09 2:08 PM, "Davide Sassera" <davide.sassera@xxxxxxxx> wrote:
> 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 Davide 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
>
> Davide
>
>
>
>
> G
> 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
>>
>> Giuseppe
>>
>>
>
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