[Artemis-users] Java web start with Artemis

Hi I would like to be able to serve up genomes with BAM files as shown in http://www.sanger.ac.uk/resources/software/artemis/ngs/. It is very handy for our end-users to be able to visualize the a NGS alignments in a familiar tool. Is there a how to set up artemis with Webstart and bam files l

[Artemis-users] Conversion of GFF3 into EMBL multiple files

Is there a way to convert multiple GFF3 files into EMBL format with the correct "join" for euk. CDSes? Artemis is able to correctly read and write the GFF3 /EMBL file I have but how do I do this for multiple contig files. Bioperlish options seem straightforward for a one exon ->one CDS mode. I

[Artemis-users] BamView counts/rpkm in Artemis

Is there a way to get all the counts/rpkms generated by loading the BAM file in Artemis extracted for all CDSes? Thanks Preethi ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users

Re: [Artemis-users] Artemis Export EMBL From GFF

Trying to do the same thing, multiple contigs GFF3 file with FASTA included. GFF has only gene/mRNA/exon/CDS calls trying to convert into EMBL. Gets to the export point and then complains that destination format cannot handle keys/qualifiers and then nothing... Also the Write amino-acids to qu

[Artemis-users] MAGPIE .. artemis

Hi   Has anyone tried out the MAGPIE/bluejay system out of http://magpie.ucalgary.edu and compared ease of use/feature sets with artemis (web-based)  or apollo -based system for annotating microbial genomes. I am interested in your experiences and what your conclusions were.   Specifically

[Artemis-users] CHADO connectivity

Hi I am following up on a post I made in Jan 2006. I am currently trying to use Artemis8 and GFF3. We are planning on using the CHADO schema from GMOD and also, Gbrowse. We have the CHADO/Gbrowse part working with some test GFF3 data that we have adapted from the Artemis GFF3 dump. Is there any p

RE: [Artemis-users] database

Hi Has anyone converted Artemis GFF into 1. Apollo compatible GFF 2. Gbrowse compatible GFF There seems to be several quirks specific to each flavor of GFF. Makes life difficult! Tim, its great to know that database connectivity(CHADO) is going to come our way soon. Any thoughts on how soon

RE: [Artemis-users] Window placement request

Hi, I use a similar set-up dual monitors and that would be a nice to have feature in Artemis. :-) Preethi -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Brooke Peterson-Burch Sent: Friday, March 25, 2005 12:24 PM To: artemis-users@sanger.ac.uk Subject: