User: spanakorice

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spanakorice10
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Posts by spanakorice

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Generation of gene panel based on HPO terms
... Ideally I would like a tool to provide me dynamic gene panels based on my HPO terms. Usually I do not have access to bioinfomatic data but would wish to get some ideas and/or provide the gene panel to my colleagues for analysis. Commercial gene panels are already available but often not exhaustive ...
written 4 months ago by spanakorice10
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Comment: A: Generation of gene panel based on HPO terms
... Anyone. Any idea? (20 characters) ...
written 4 months ago by spanakorice10
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Generation of gene panel based on HPO terms
... Hello. I would be interested to know if there are publicly available tools for generating gene panels based on HPO terms. Something similar to PhenoXome ( https://phenoxome.chop.edu/phenoxome/index.jsp ) or XomeDxSlice ( https://www.genedx.com/xomedx-slice-tool/ ) but rather more uptodate. For so ...
gene ngs written 4 months ago by spanakorice10
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Comment: C: How do I make a schema with all described variants within a gene?
... Thank you. MutationMapper seems to do what I was searching for! I still have to try with my data. ...
written 8 months ago by spanakorice10
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How do I make a schema with all described variants within a gene?
... Hello. I would like to make a graphical representation of a transcript with all known variants. Something similar to image below. Would anyone know how this can be done (apart from the "add custom tracks" of UCSC genome browser)? Thank you in advance. ![enter image description here][1] [1]: h ...
gene variants schema written 8 months ago by spanakorice10 • updated 8 months ago by WouterDeCoster31k
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Comment: C: NGS statistics - Mean coverage and % of bases >20x (or probability to miss one o
... Thank you Kevin. I am afraid it is not that simple. There was a recent talk at the ESHG meeting from A. Rauch citing the NGS guidelines I mentioned above. The following stats are from the guidelines. gif image host So the discussion was that - in the clinical setting - it is better to "throw" you ...
written 10 months ago by spanakorice10
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Comment: A: NGS statistics - Mean coverage and % of bases >20x (or probability to miss one o
... It's just that different options eg. 65x and 130x are often offered from the same lab for different prices (the latter being 50% more expensive). For the 130x mean coverage they give ~96-97% above 20x. So I was wondering what the % of 20x coverage would be for the 65x exome. And if this can be also ...
written 10 months ago by spanakorice10
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Comment: A: NGS statistics - Mean coverage and % of bases >20x (or probability to miss one o
... Would anybody have an idea? ...
written 10 months ago by spanakorice10
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NGS statistics - Mean coverage and % of bases >20x (or probability to miss one or two variants)
... Dear colleagues, I would be interested to know if there is a publication or other reference for NGS statistics. The NGS guidelines published in 2016 (PMID: 26508566) provide an estimate of probability to miss a variant in different situations, namely considering the % of bases covered >20x. Eg. ...
next-gen sequencing written 10 months ago by spanakorice10

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