Visualization Of Sequencing Data From Bacteria (Prokaryotes)

Question

[kanwarjag]

I want to visulaize bam/ sam files of RNAseq data of a bacteria. Is there a good easy to use tool (like IGV). I read one post -Which genome browser works best with prokaryotic genomes and data but could not found something very user friendly or easy to navigate. Any suggestion?

[Giovanni M Dall'Olio]

which kind of visualization do you have in mind? Basically, you are saying that you want to visualize BAM files, but not with a Genome Browser. Can something like Circos be useful for you?

[kanwarjag]

Thanks. Just like when we are working with human genome we upload the bam files to IGV or ucsc genome rowser to see what is happening to a particular gene, what is pattern of reads in two samples, coverage etc (e.g Fig 1 of this paperhttp://www.nature.com/nbt/journal/v29/n1/abs/nbt.1754.html)

Answer 1

[Torst]

These are the freely available genome viewers that support BAM that I have tried over the last ten years:

• Artemis http://www.sanger.ac.uk/resources/software/artemis/ (the traditional Bacteria genome viewer)
• BamView http://bamview.sourceforge.net/ (based on Artemis)
• Tablet http://bioinf.scri.ac.uk/tablet/ (reads Velvet .afg files too)
• Hawkeye http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye
• Eagelview http://bioinformatics.bc.edu/marthlab/EagleView
• IGV http://www.broadinstitute.org/igv/ (has become standard viewer for eukaryotic genomes now)
• Apollo http://apollo.berkeleybop.org/current/index.html

We tend to use Artemis and IGV, depending on what we want to do. Artemis can get slow viewing paired-end BAM reads, but it has lots of cool features specifically for bacterial genomes that we miss in IGV.