Marusia
Is there a tutorial on how to use genome explorer? When im using my 23andme "explorer" I can easily find any gene that was checked and Im interested in. On contrary I just can't undersrand how dante labs genome manager works nor is it explained in any tutorial/ video.
Quote 0 0
Clare86
@Marusia The DNA explorer is an implementation of the web version of IGV (Integrative Genomics Viewer). There is a website that provides information on using the desktop version, https://software.broadinstitute.org/software/igv/, but this assumes some knowledge of genetics.

When using the DNA Explorer in the Dante's Genome Manager you are viewing the contents of your Bam file. In the input box that I've shown a screenshot of below you can search for genes or for chromosomes and positions. You can't search for rsids.
Screenshot 2020-07-10 at 15.25.20.png   
In the case of a small gene you will see something like the below. With larger genes you will be told to zoom in to actually see anything. The top part is a bar chart showing the read depth at each position and shows SNPs where one differs from the reference genome. You should be able to see a bar below that is half red and half blue. This represents a heterozygous variant I have in this gene.

The viewer is helpful for looking up specific positions and looking at the reads at that position but if you're looking to find all the variants you have in specific gene then you would be better off using the vcf file. If you are looking for something like 23andme's browse raw data page then I suggest uploading your vcf files to sequencing.com and using their genome explorer app.
Screenshot 2020-07-10 at 15.28.55.png 
Quote 0 0