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; email@example.com 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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