I have sequenced partial mitochondrial genome of Philautus sp. and have generated a consensus representing the reconstructed genome from the reads. There are many single nucleotide variants present when compared to a reference genome. How can I visualize these SNVs without a reference genome as genome browsers like IGV require reference genomes?
I figured it out, thanks for the reply Mathew A Beale, I was able to map the reads to my consensus and then used it reference, earlier I wasn't able to open my consensus in IGV since I am using for the first time and not much familiar with it.
Hi Debjoyti,
If you want a quick and easy access to a genome browser, specially for smaller genomes, I suggest your try Artemis (http://www.sanger.ac.uk/science/tools/artemis).
You can start right from a FASTA file for your genome and a BAM file for your mapping. It has good visualisation and it's light weight.
Anna
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