Re: [AMOS-help] How to convert a file to prefix.1con file

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

Hi Tram,
The .1con file is just a fasta formatted file containing the reference
sequence. That's an outdated suffix used by TIGR that means "one contig"
(1con) in fasta format. That's even misleading because AMOScmp can also use
a multi-fasta file as the reference.

Best,
-Adam


On Wed, Dec 29, 2010 at 4:08 PM, Tram Ta <myt...@gm...> wrote:

> Hi, thank you for looking at this post.
>
> I am using Amoscmp-shortread-alignment-trimed to assemble a bacteria genome
> and have a question about the "xxxx.1con" file. As I read, the reference
> genome should be in format xxxx.1con, and I did search online to find how to
> convert to this file format but there is no help.
>
> I ran the Amoscmp-shortread-alignment-trimed, using Amos-message file for
> the target, and a fasta file for reference, and Amos didn't complain, it
> worked. So my questions are:
>
> 1. Is it Ok to use a fasta file for the reference genome?
> 2. And how to convert a file (fasta, ...) to the xxx.1con file (if there is
> already explanation for this, please show me the link)?
>
> Thank you in advance (your answer will save me a lot of time to search) :)
>
>
>
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