Does anyone know of a BAM/SAM alignment viewer that shows the location of alignments on the query as well as the reference? I'm looking at alignments from long reads (PacBio) to a reference, and there are multiple separate alignments for each read (think cDNA aligned to genomic reference) ... so I want to see the order, orientation, and spacing/overlap of all of the alignments on the reads, as well as on the reference.
I have never heard of a tool that does that. The Integrative Genome Viewer tool from Broad is pretty handy for viewing a quick alignment to some reference. You can load your own reference for example. One hacky work around would be to use some set of your pacbio reads as the reference, and then align your other pacbio reads to that. Then you can load that as the reference in IGV, and view that alignment. That sounds less than ideal though. At the very least IGV is a great tool for viewing BAM alignments. You can even launch it through an SSH tunnel. If you haven't done that before you can do it by logging into the server that has your data with
ssh -X user@domain and then running
javaws igv.jnlp where the
.jnlp file is the thing that is linked to by the button to
Launch the viewer from the download page of the IGV website. You can right-click on the launch button, copy the link, download it to the remote server with
wget and then run IGV remotely using javaws (the command line way to call java web start).