Entering edit mode
11.4 years ago
kanwarjag
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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?
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)