Hi Tim, You made my day. You are simply awesome, as always. Thanks so much,
Gowtham ________________________________________ From: Tim Carver [...@sanger.ac.uk] Sent: Wednesday, November 10, 2010 7:52 AM To: Gowthaman Ramasamy; artemis-users@sanger.ac.uk Subject: Re: [Artemis-users] Command line options to load BAM files and zoom to a gene Hi Gowtham You can do this now. I have just added the option to load the BAM's from the command line - it has been on the list of things to do. You can get the latest development version (v12.1.11) from: ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/development/ Using -Doffset you can set the base position it opens at. Using -Dbam you can specify the path to a BAM (or list file of paths to bams). The syntax will then be something like this: java -Doffset=12500 -Dbam=/path/file.bam \ -jar artemis_v12.1.11.jar foo.embl + foo.gff Or with the 'art' script: ./art -Doffset=12500 -Dbam=/path/file.bam ~/foo.embl + ~/foo.gff Regards Tim On 11/9/10 11:54 PM, "Gowthaman Ramasamy" <gowthaman.ramas...@seattlebiomed.org> wrote: > Hi All, > I am wondering if the following can be achieved by command line options > alone. > > I would like to load a gff file (with sequences), and load two or more .bam > files and to navigate to gene of interest. (controlling zoom level, if that is > not too much to ask). > > As you might have guessed it from now, I would like to make the job of some > scientists in our lab bit easier by pre-configuring everything. So, that they > fire a command / click a link, they are taken to Artemis and to the region of > their interest. So, if anyone has any other way to achieve it, i will really > appreciate it...... > > > Thanks so much in advance, > Gowtham > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
