User: CY

gravatar for CY
CY10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
4 days, 9 hours ago
Joined:
1 year, 6 months ago
Email:
c*******@gwmail.gwu.edu

Posts by CY

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Somatic variant caller
... Very precise explanation. Thanks ...
written 4 weeks ago by CY10
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Somatic variant caller
... We are using Illumina's Somatic Variant Caller (https://www.illumina.com/documents/products/technotes/technote_somatic_variant_caller.pdf) to call somatic variant from tumor sample. Based on the Somatic Variant Caller description, it used Poisson model to calculate p-value for each variant to be tru ...
variant calling somatic next-gen written 5 weeks ago by CY10 • updated 5 weeks ago by markus.riester70
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Distribution of somatic mutation
... So... I got two questions. 1) Does somatic mutation follows poisson like germline mutation does? 2) We now use bayesian model to detect germline mutation. Does the mutation have to follow specific poisson distribution in order to use bayesian model? If it does not, can we use bayesian model for so ...
next-gen snp written 5 weeks ago by CY10 • updated 5 weeks ago by solo777330
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Comment: C: Call variant from RNA-Seq data using Haplotypecaller
... Since we use GATK, a DNA-Seq variant caller with a probability model based on DNA allele frequency, to call variant on RNA-Seq, I imagine there will be lots of false negative (no expressing allele missed and allele with weird frequency in the sense of DNA allele frequency missed). However, there wil ...
written 5 months ago by CY10
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Comment: C: Detecting variants at very low fractions from ctDNA
... FreeBayes and VarScan are for detecting somatic mutation from tumor sample indeed. I am wondering if there is any variant caller that is specifically designed to detect variant from ctDNA (very low variant allele fraction) ...
written 5 months ago by CY10
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Detecting variants at very low fractions from ctDNA
... The variants detected fro ctDNA are at very low fractions. So my question is: Can anyone share some insight on how to distinguish between variants at very low fractions and noise (perhaps sequencing error)? It will be really helpful if one or two software are recommended specifically for detecting t ...
ctdna mutation variants written 5 months ago by CY10 • updated 5 months ago by Tonor390
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Comment: C: 11% mutation frequency of TP53 in non-cancer samples
... Could you share some details of your pipeline for detecting variants at very low fractions. I am currently researching on this and like to have a optimized pipeline set up. Really appreciate :) ...
written 5 months ago by CY10
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Comment: C: Call variant from RNA-Seq data using Haplotypecaller
... Yes, Your way could be a solution. Could you share more details on the 'allele specific expression analysis'? maybe a recommended pipeline or something. That will be really helpful :) ...
written 5 months ago by CY10
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RNA expression profile for tumor sample OVER TIME
... I feel like this maybe a naive question: I imagine that RNA expression of tumor is dynamic. Can any one share some comments on the variability of the expression profile of tumor over time? My assumption is that, if the expression profile is relatively stable, it is worth the research for tumor expr ...
tumor rna-seq expression written 5 months ago by CY10
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Comment: C: Call variant from RNA-Seq data using Haplotypecaller
... Yes. They are. My point is that there are too many complications involved to accurately call variants from RNA-Seq of tumor sample. ...
written 5 months ago by CY10

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