[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 loaded per genome- how do you get from my genome file and the correspond .bam and .bai to the jlnp file that is needed by the web start. - its probably obvious but I am new to web-start and would appreciate any help. The server is running Ubuntu with Apache as the web server. It is set up with the right mime types for Java Webstart. Thank you Preethi Best Regards Preethi Ramaiya ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[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 have Parent and ID tags in gene/transcript/CDS structure Thanks Preethi ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[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 qualifier - using the GFF3 file writes the translation to the exon features rather than the CDS and then the resulting file is unreadable by artemis. Version 12.0.1 >From the link that Tim posted. Any pointers...would it help to split the fasta+GFFs for each contig ? Many thanks Preethi ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[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 for a community based annotation effort where it will be necessary for third party editing of things like gene-names, functions etc but not necessarily of sequence data itself. Preethi ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[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 plan to get CHADO connectivity in Artemis soon..? :-) That might save us an Artemis->Apollo migration. We like the user interface in Artemis (bacterial genomes) and would like to have a straight pipe into CHADO. Thank you! Regards Preethi - "Hi Preethi I plan to get a Artemis/ACT release out in the next couple of months (hopefully sooner than later). To get it talking to CHADO it has become more GFF3 compliant which is what we are working towards but this has not been used in anger yet. Regards Tim" ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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 this might get into Artemis.. :-) Preethi -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of biarshin Sent: Thursday, January 26, 2006 6:50 AM To: Artemis-users@sanger.ac.uk Subject: [Artemis-users] database I would like to set up a database for a small community studying a model organism. We would we like to have a small database running on our server that the community could access using Artemis. Users would use Artemis for doing gene annotations and browsing the genome. Ideally the users would have the option of either connecting to the online database or using a cached copy of the database residing on their local computer (which could be in flat file format since it would be a single user environment). My question is has anybody set up such as system using Artemis, and where might I get information on how to set it up. Specifically is there information available on how to set up a a centralized database for our genomic information that the users could browse with Artemis? Thanks, Brad ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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: [Artemis-users] Window placement request I have a feature request that won't kill me to have ignored by the developers if its a huge bother since I'm probably in a minority of the userbase and its just a mild annoyance. Certainly, the other scientists I've gotten to use Artemis locally don't share this setup. My request is that the developers keep in mind the location where the user placed the last instance of a window when opening new windows of a similar type. This is not an issue when windows are simply hidden upon close. The systems I use when working with Artemis have a dual-monitor setup. Because Artemis tends to open dialogs in a screen-centered position rather than relative to the parent or application window, they are always nicely split by the borders between the two monitor screens and must be dragged to the viewable area of one monitor or the other in order to be sensible. For example, there are many activities in using the application where I sequentially open a large number of windows to look at the information for some features or compare them. In my own java applications I usually track placement with a rectangle so that any user-invoked resizing is not lost either. A Point marking the current window origin would work nicely as well but I just track the bounds rectangles so I can reuse a single code snippet to place the windows. This may not affect enough users to be worth any coding time. Just sharing an "I wish..." that frequently runs through my mind when working with Artemis. :o) -=Brooke ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
