Re: [AMOS-help] AMOScmp scaffolding

[Adam P. <aph...@gm...>]

You can try 'bank-report -b your.bnk SCF' to dump the full information for
the scaffolds. That will be an AMOS formatted message file containing quals,
offsets etc. The format is similar to the Celera Assembler messages, if you
are familiar with them. It should contain everything you need. 'bank-report
-b your.bnk' will dump all the assembly info (including reads and contigs)
if you need it to be all in one place.

-Adam


On Thu, May 28, 2009 at 9:25 AM, Brian Haas <bh...@br...> wrote:

>
> Hi Adam,
>
> I'm trying to figure out the best way to extract the scaffolding
> information from the assembly.  Do I get this from the .layout file?  Is
> there another file, or agp-type equivalent?
>
> Here's what my .layout file looks like:
>
> C 1     1       128433_Escherichia_coli_K12_str 8-802
> 1 0 794 0       0       99.3734
>
> C 2     1       128433_Escherichia_coli_K12_str 810-1513
> 2 703 0 0       0       98.7234
>
>
> I'm not sure how to decipher it, though.
>
>
> Thanks for your help.
>
>
> Best,
>
> -b
>
>
>
> --
> Brian J. Haas
> Manager, Bioinformatics Outreach, Genome Annotation and Analysis
> The Broad Institute
> http://broad.mit.edu/~bhaas <http://broad.mit.edu/%7Ebhaas>
>
>
>
>
>
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