Visualization Of Sequencing Data From Bacteria (Prokaryotes)
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11.2 years ago
kanwarjag ★ 1.2k

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?

visualization sequencing bacteria • 4.1k views
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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?

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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)

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11.2 years ago
Torst ▴ 980

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

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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