Re: [AMOS-help] Displaying my own features in hawkeye

[Michael S. <mic...@gm...>]

Hi Karen,

The easiest way to load custom features is to use the tool loadFeatures.

The input is a simple tab deliminated file with the following fields:

contigeid type end5 end3 [comment]

contigeid is the contig which has the feature
type is the single character feature type.
end5 and end3 are the coordinates of the feature
[comment] is an optional comment string describing the feature

Standard types are:
 (B)reakpoint
 (C)overage
 (O)rf
 (S)NP
 (U)nitig

For example, this line creates a custom snp feature between positions 1000
and 2000 on contig 1234

1234 S 1000 2000 Lots of SNPs

Once you have your file of features, just run:

$ loadFeatures bankname featfile

There are a few options:

   -u Coordinates are ungapped
   -i Contigid is the IID

Good luck!

Mike Schatz


On Mon, Feb 15, 2010 at 4:29 PM, d f <df6...@gm...> wrote:

> Hi,
>
> The AMOS Hawkeye website says that "users can easily load new metrics
> via an XML-like interface" into hawkeye.  How do I do this?
>
> What I am trying to do is this: I have a 454 Newbler assembly and I am
> trying to assess its quality. I've used amosvalidate to do most of the
> validation, but amosvalidate doesn't assess mate-pair happiness with 454
> mates.  To get some idea if there are regions of the assembly that have
> a high density of unhappy mates, I'd like to display the unhappy mates
> identified in 454PairStatus.txt using hawkeye.  In other words, I'd like
> to display user-generated data on hawkeye.
>
> Karen :)
>
>
>
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