Hi Tony If you look at the BamView website: http://bamview.sourceforge.net/
Under the 'Generating a BAM' tab there are examples there. This command should sort the BAM for you: samtools sort file.bam file.sort.bam This command will produce the index (.bai) file: samtools index file.sort.bam The index file needs to be in the same directory as the BAM file and you do need to be running Artemis with Java 1.6. Regards Tim On 2/3/10 1:34 AM, "Tony Barbet" <abar...@nersp.nerdc.ufl.edu> wrote: > Tim, > > Re-this thread: > > We have generated a BAM file of 454 reads aligned with a reference > sequence using the latest version of Mosaik software, but I am unclear > on the exact Samtools commands that would convert this into a BAM file > suitable for Artemis (sorted and indexed). Is there some info on this? > > Thank you for your help. > > Regards, > > Tony Barbet > > > > > Tim Carver wrote: >> Hi Gowtham >> >> Have a look at BamView. >> >> http://bamview.sourceforge.net/ >> >> This is integrated into Artemis and can be found in the Artemis development >> version (which is available from the above link as well as the Artemis home >> page) and will be in the next release. >> >> Regards >> Tim >> >> On 1/26/10 8:07 PM, "Gowthaman Ramasamy" <gowthaman.ramas...@sbri.org> >> wrote: >> >> >>> Hi Tim, >>> I am trying to see if we can use artemis to display aligned illumina reads >>> against a chromosome. I know we can make user plot and display coverage >>> information. But wondering is there a way to display the reads themselves >>> (nt >>> seq). >>> >>> Gowtham >>> >>> >> >> >> >> _______________________________________________ >> 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
