Visualization Of Sequencing Data From Bacteria (Prokaryotes)
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?
1 answer
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.
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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?
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)