Re: [AMOS-help] AMOS/Hawkeye Features

[Michael S. <ms...@um...>]

Hi Sven,

Features are just a way of recording regions of interest in your
assembly. We commonly use features to mark regions that look
mis-assembled, but you can also use them to store the locations of
genes, regions that align to another genome, or any other
characteristic you may be interested in. You can graphically display
features in Hawkeye, and get textual reports via dumpFeatures. You can
load custom features using the tool 'loadFeatures' which takes a
simple tab deliminated file with one feature per line. See
'loadFeatures -h' and 'dumpFeatures -h' for more info.

The easiest way to create mis-assembly features is to use our
mis-assembly pipeline: amosvalidate. Given a bank called
'assembly.bnk', run 'amosvalidate assembly.bnk'. It will then process
your assembly to find regions that have mis-assembly characteristics
such as regions with compressed mates, unusually high coverage, or
correlated SNPs. The last stage of the pipeline is to combine the
individual lines of evidence (coverage, mates, SNPs, etc) into a
single file of the most suspicious regions which will be called
assembly.suspicious.regions that makes a good start towards cataloging
the potential mis-assemblies. In our tests the sensitivity is quite
high (basically all mis-assemblies are flagged), but the specificity
can be more variable. In the first display in hawkeye, the contigs and
scaffolds with the most mis-assembly features will be colored the
brightest shade of red. These are often the most likely to be
mis-assembled.

Let me know if you have any more general questions about features. I
can also send you a preprint explaining how the mis-assembly features
are computed if you are interested.

Hope this helps,

Mike Schatz


On 10/4/07, Sven Klages <kl...@mo...> wrote:
> Dear all,
>
> I was wondering where to find documentation
> on how to create "features", or more general,
> what are "features" ?
>
> Currently I use CA input(frg)/output(asm) to
> create AMOS banks.
>
> Any help is appreciated,
>
> tia,
> Sven
>
> --
>  Sven Klages
>  Max Planck Institute for Molecular Genetics
>  Ihnestrasse 63/73, 14195 Berlin (Dahlem), Germany
>
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