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From: Adam P. <aph...@gm...> - 2011-01-05 15:09:00
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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 That's an outdated suffix used by TIGR that means "one contig" (1con) in fasta format.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) :) > > > > ------------------------------------------------------------------------------ > Learn how Oracle Real Application Clusters (RAC) One Node allows customers > to consolidate database storage, standardize their database environment, > and, > should the need arise, upgrade to a full multi-node Oracle RAC database > without downtime or disruption > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help > > |