Don't know if this helps, since it is slightly different to the problem you 
mention, but this worked for me to produce a file to look at Bam files mapped 
against all 14 Plasmodium chromosomes concatenated in Artemis, sequences + 
annotations :

1. Save files of individual chromosomes in Artemis as embl format
2. Use program yank to make list file of the individual chromosome file names, 
cds.list
3. Do union -sequence @cds.list -sformat embl -outseq Pfall.embl -osformat embl 
-feature -auto
4. Open Pfall.embl in Artemis


Tony Barbet
________________________________
From: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk] 
on behalf of Tim Carver [t...@sanger.ac.uk]
Sent: Tuesday, February 25, 2014 4:51 AM
To: Steven Sullivan; artemis-users@sanger.ac.uk
Subject: Re: [Artemis-users] loading a eukaryotic genome assembly(multifasta) 
and annotation into Artemis 16.0.0


In Artemis, with a multi-fasta sequence file, the options for the annotation 
file are to use a GFF file or to in some way to concatenate the EMBL/GenBank 
feature table (adjusting the coordinates to match the correct position of the 
assembly). This is what ‘union’ should do with EMBL files. I am not sure why 
this wasn’t successful for you.  You obviously do need to use ‘-feature’ with 
union to get the feature table included:

union –feature –osf embl  entry.embl

Using GFF and union are the options used here.

Regards
Tim

On 24/02/2014 20:05, "Steven Sullivan" <sulli...@nyu.edu<UrlBlockedError.aspx>> 
wrote:

ENA (EMBL) provides TEXT and FASTA file downloads for eukaryotic assemblies.  
The FASTA download is single a multi-fasta file containing separate records for 
each chromosome. The TEXT download is a single EMBL feature table concatenating 
all the feature tables of the individual chromosomes.  It does not contain the 
DNA sequence.

Loading these two files into Artemis yields a view of the entire assembly as a 
concatenated sequence, but only the features for the first chromosome in the 
feature file are loaded.

I understand that this issue has been brought up before. (e.g. 
https://www.mail-archive.com/artemis-users%40sanger.ac.uk/msg00690.html)  What 
I don't see is a workaround.  Mention was made of the EMBOSS 'union' command, 
which I have tried,  but I  am unable to make that generate an .embl file that 
contains the correctly remapped coordinates of the features onto the 
concatenated sequence. The closest I came to success was an .embl file that 
mapped the first chromosome features only , and incorrectly, onto the 
concatenated sequence.


Is there a 'correct' way to do load a multifasta record and its annotation into 
Artemis?  The Artemis user manual is rather opaque on this topic.

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