User: rb14sp

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rb14sp40
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Posts by rb14sp

<prev • 14 results • page 1 of 2 • next >
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NextSeq indel Concordance with Plat genome or NIST
... Hi, I was wondering if anyone has had experience doing concordance with samples sequenced on nextseq machine. I'm finding the False Negative rate with indels to be high (15-19%), higher than for the hiseq. I was using GATK GenotypeConcordance with both Platinum genomes and Nist truth sets. We seq ...
nextseq illumina indels written 8 months ago by rb14sp40 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: Sanger validated SNP not present in IGV despite 10X coverage at site??!!
... No sample swap, we've confirmed ...
written 9 months ago by rb14sp40
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Sanger validated SNP not present in IGV despite 10X coverage at site??!!
... Hi, Sanger validation has shown that there is a c.26T>C variant detected in REEP1. The genomic coordinate is chr2:86564608. There is a read depth of ~10 at this position but no variant. Will someone offer their thoughts about this and why it was not picked up by exome sequencing? Thanks - Ro ...
sanger ngs igv written 9 months ago by rb14sp40 • updated 9 months ago by finswimmer7.9k
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Question: Gene Ontology Enrichment using Constrained Genes as Reference Set; P-values = 1
... I'm trying to do gene set enrichment analysis using the set of constrained genes from ExAC (pli >= 0.9 || mis-z >= 0.3) as a reference list (attached), as I did not look at missense in genes with mis-z < 0.3 or undefined and I did not look at PTVs in genes with pli < 0.9 or undefined in ...
gene set enrichment analysis gene ontology go written 15 months ago by rb14sp40
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Comment: C: Gene set enrrichment, GO; Comparing Effect Size between two groups
... o.k I just used Fisher's Exact test to test for a difference between groups ...
written 15 months ago by rb14sp40
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Gene set enrrichment, GO; Comparing Effect Size between two groups
... Hi, I have two gene sets ( A and B). Set A is significantly enriched for GO terms (e.g., nervous system development) while C2 is not. But I can't make the mistake of comparing p-values between groups. I need to compare effect sizes between groups. Is the effect for group A greater than group B. D ...
comparing effect sizes go gene set enrichment written 15 months ago by rb14sp40 • updated 15 months ago by genomax59k
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ExAC pLI question for AKAP9
... Hi, Looking at ExAC I see that the pLI is 0 for AKAP9 and yet the observed number of LoF variants (38) is much less than expected (140). Can someone explain this? Why would the pLI be 0 in this case? There's other genes likes this as well. Thanks. - Robert ...
exac written 17 months ago by rb14sp40 • updated 17 months ago by Biostar ♦♦ 20
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Comment: C: Rare Variant Association Tests and ExAC Data Set
... Hi, thanks for the response. clustering of the samples was already done and they are all of European ancestry getting more controls is not an option ...
written 18 months ago by rb14sp40
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Comment: A: Rare Variant Association Tests and ExAC Data Set
... Oh and I see Daniel MacArthur's name is on the Barret et al. paper as well. I think he's just warning people to be cautious. In my case I think this step is at least reasonable. ...
written 18 months ago by rb14sp40
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Answer: A: Rare Variant Association Tests and ExAC Data Set
... This issue came up recently in connection with a high profile targeted sequencing study in autism by Stressman et al. which was retracted due to statistical flaws. Stressman et al. also did a case/control analysis using the ExAC data and Barret et al. 2017 was critical of that decision as well but n ...
written 18 months ago by rb14sp40

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