User: GabrielMontenegro

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Posts by GabrielMontenegro

<prev • 108 results • page 1 of 11 • next >
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Comment: C: How to estimate significance of RPKM value on GTEX
... Reading the GTEX Science paper (http://science.sciencemag.org/content/348/6235/648/tab-pdf) I have seen that they mention a "minimal treshold reads per kilobases per millon mapped reads (RPKM) > 0.1". Does this mean that in order to say that a tissue is expressed needs to have at least 0.1 RPKM? ...
written 7 days ago by GabrielMontenegro330
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How to estimate significance of RPKM value on GTEX
... After conducting a GWAS I have a set of SNPs and a set of genes that were significantly associated to my trait. I want to know if the genes that I have found are significantly expressed on the tissues present in the GTEX database. I have never worked with expression data before, and I don't even kn ...
gene expression rna-seq written 9 days ago by GabrielMontenegro330
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Comment: C: Plink genotype data (based on SNP) format!
... Could you provide an example of your data? ...
written 11 days ago by GabrielMontenegro330
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Answer: A: Calculating ethnicity of a sample VCF
... If you want to get ancestry estimates for your sample, probably the easiest way would be to do that using ADMIXTURE, a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estima ...
written 11 days ago by GabrielMontenegro330
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Answer: A: Is it possible to use haplotypes instead of SNPs for association testing with ph
... If by genomic selection you mean using haplotypes to find signatures of selection, then the answer is yes. Many popular haplotype-based tests are conducted using haplotype data. From the top of my head: iHS, nSL, XP-EHH. There are probably many more. Doing GWAS with haplotypes is also possible and ...
written 13 days ago by GabrielMontenegro330
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Comment: C: Deciding on a hardy-weinberg filter for case-only dataset
... An actual association can cause deviations from HWE. I am not sure whether you would actually want to filter those SNPs. Why not just flag them for further analysis (for instance to check if the deviation was caused by genotyping errors, in case they were genome-wide significant? Have you checked th ...
written 22 days ago by GabrielMontenegro330
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Answer: A: how to GWAS of characters with normal distribution?
... The easiest way would be use a **linear regression model.** One of the most popular softwares to conduct GWAS is by far PLINK: https://www.cog-genomics.org/plink2 Before doing the GWAS, however, you should do various QC steps. I recommend you to read this tutorial by D. Balding: http://www.nature ...
written 26 days ago by GabrielMontenegro330
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Meaning of "EX_TARGET" in VCF files 1000 genomes
... I am working with some 1KG VCF files and I just extracted biallelic SNPs using the `vcflib` library. However, I noticed that some SNPs have this additionally field: "EX_TARGET" ...SAS_AF=0.001;VT=SNP;EX_TARGET GT 0|0 0|0... I've googled it and however I haven't found it anywhere on the 1KG doc ...
genome vcf written 12 weeks ago by GabrielMontenegro330 • updated 12 weeks ago by Pierre Lindenbaum96k
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Single-Tissue eQTLs: P-value threshold in GTEX ??
... Hi all, eQTL is not my area of research, however I am interested to see if a particular SNP has a significant expression in the GTEX database. I have queried this SNP rs4888622 (found on a paper on gene expression on the human brain). This is the result: (link: https://www.gtexportal.org/home/snp ...
snp rna-seq written 3 months ago by GabrielMontenegro330
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Getting Precomputed Conservation Scores
... I have a list of millions of SNPs (rs IDs) and I wanted to know if these are highly conserved sites based on conservation metrics, for example: PhastCons, GERP or SiPhy scores. I was trying to find precomputed scores for these metrics, but wasn't very successful at finding them. I could find preco ...
genome conservation snp written 3 months ago by GabrielMontenegro330 • updated 3 months ago by Santosh Anand2.9k

Latest awards to GabrielMontenegro

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Popular Question 3 months ago, created a question with more than 1,000 views. For Using Ldhat To Estimate Effective Population Size
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Scholar 5 months ago, created an answer that has been accepted. For A: How to convert input files from PLINK to snp.plotter?
Popular Question 5 months ago, created a question with more than 1,000 views. For Using Ldhat To Estimate Effective Population Size
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