Re: [Mauve-users] exported gaps and annotations
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koadman
From: Aaron D. <aar...@ut...> - 2016-10-17 18:32:05
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Hi Thierry, good question about the gap file & column headers. The first columns are as described by the file headers. The subsequent columns come in triplets, one triplet for each aligned genome, containing the following information: 1. The genomic position of the gap 2. The name of the chromosome where the gap is located 3. The contig-local position of the gap I agree this is confusing and this information should be added to the file headers in a future Mauve release. As for your second question, there is currently no way to produce a reordered GenBank format file with the contig mover. If you've got automatically generated annotations, then if possible I would suggest running the annotation after reordering contigs. Best, -Aaron On Wed, 2016-10-12 at 17:09 +0200, Thierry K.S. Janssens wrote: > Dear Dr. Darling/Aaron, > > I have a small question regarding the interpretation of the > coordinates > in the exported gap file. > The headers in this tab delimited file is less than the nuber of > colums. > This makes the interpretation cumbersome. > > Could you also give a hint how to maintain the annotations in from > the > Genbank, beyond the first iteration of the contig reordering? > > Thank you in advance for a short explanation on this. > > kind regards, > > Thierry Janssens > > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |