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Visit our Genomics page and click on ‘WTC whole genome’. This will direct you to our UCSC genome browser tracks for WTC11.
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Now scroll down to the track section below the browser (section with blue horizontal bars) and click on ‘WTC (parental) genome…’ and select “show” and submit
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Scroll back up to the top of the page, and you should see two tracks for WTC11: WTC parental line variants and WTC whole genome alignment. The variant track shows all of the WTC variants (SNPs and short indels) relative to the GRCh38 human reference genome.
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Observe the reference genome sequence that now includes WTC specific variants. Unfortunately, that sequence is unable to be directly downloaded, but to get that info do the following:
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Using the search bar, look up the MAPT gene or by using the ‘Blat’ function (under Tools), look up the sequence of your homology arms. Note: there may be no WTC specific variants or a small number of variants depending on the precise location and size of your homology arms.
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You may download the reference sequence by going to View -> DNA -> get DNA.
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Using your own DNA editing software (i.e., SnapGene or ApE), you may modify the sequence to include the WTC specific variants if there are any. Note: the variant track includes all variants that were initially called including some that were subsequently filtered out; also variants that pass filtering will say ‘Filter: PASS’ (click on each variant to check), and only include variants that pass filtering.
Additionally, consider whether to include both heterozygous and homozygous variants, or homozygous only (e.g., we include only homozygous variants in our homology arms).
Reach out if you need any additional help with configuring/viewing the tracks.