Hi Feifei Artemis is optimised already so that it loads into memory only the reads that are visible in the display, i.e. for the region you are looking at.
If you have not already done so you should look at increasing the memory available to Artemis. See below for instructions on how this can be done for each operating system. You may also want to avoid zooming out too much in particularly high coverage regions, although Artemis will switch to a coverage view so less memory is required. Also I would recommend you investigate the read filter options in the BamView window. If you right click on the window with the reads in, there is an option to 'Filter Reads...'. You can then filter by mapping quality for example. Regards Tim For UNIX: --------- Edit the 'art' script and change the line that looks like: MEM="-mx500m -ms20m" Change the first number which specifies the maximum size, in bytes, of the memory allocation pool. Append m indicate megabytes. For windows: ------------ Create a shortcut to the Artemis JAR file. Edit the properties of the shortcut and add : java -mx800m -jar to the start of the Target: field. -mx800m sets the maximum memory Java will allocate to Artemis. You will need to use the shortcut to run Artemis from then on. For MacOSX: ----------- To change the memory allocated to Artemis on MacOSX, set the value in the file Info.plist in the directory Artemis.app/Contents. Towards the bottom of the file there are a couple of lines that look like this: <key>VMOptions</key> <string>-Xmx800m</string> Changing the value after -Xmx will change the memory used by Artemis. On 9/21/11 9:12 PM, "Feifei Xu" <feifei...@ebc.uu.se> wrote: > Hi again! > > We are manually annotating a genome of around 13 Mbases. It's fine to load > only GFF3 files. But it's very slow to load the 2.5Gb .bam file of mapped > RNA-Seq data. The RNA-Seq is very important for us in manual annotation, so we > would very much like it to be loaded into Artemis as well as other GFF3 files > of gene calling evidences. > > Do you have any suggestions of how to save memory? > > I am also wondering if there is any way to examine only one scaffold at a time > in Artemis, which will certainly reduce memory usage. > Or is there any way to split the big .bam file into smaller chunks that > Artemis will still be happy with? > > Thanks! > > Feifei > _______________________________________________ > 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
