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:
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
On 11/9/10 11:54 PM, "Gowthaman Ramasamy"
> Hi All,
> I am wondering if the following can be achieved by command line options
> 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,
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