User: LNA

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LNA10
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Posts by LNA

<prev • 9 results • page 1 of 1 • next >
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SNP annotation with TFBS and histone marks
... Hi, I have to annotate a list of SNPs with information about transcription factor binding sites and histone marks. I found data for download on the UCSC webpage, but I'm hoping for a more straightforward way to do this. In another post someone recommended using the Enseml VEP for this task. Is the ...
annotation tfbs histonemarks vep snp written 10 days ago by LNA10 • updated 10 days ago by Emily_Ensembl13k
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Comment: C: Annotation of GWAS results with GTEx
... I used the GTEx_Analysis_V6_eQTLs.tar.gz from Single Tissue eQTL Data in "GTEx Analysis V6 (dbGaP Accession phs000424.v6.p1)". It was not clear to me why the V6 data provides only one file and the V6p data provides two files for cis and for trans. Finally, I used the V6 data, I don't know how much d ...
written 8 weeks ago by LNA10
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Comment: C: Annotation of GWAS results with GTEx
... My mistake... You're right, all the information is in the download section. Thank you very much for the hint. I somehow misinterpreted the description and thought all the data has to be obtained from dbGaP. Of course it would be easier if there was a the possibility to get the data for a predefined ...
written 9 weeks ago by LNA10
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Annotation of GWAS results with GTEx
... Dear all, I have a list of SNPs as a GWAS result and I would like add the information whether a SNP is a known eQTL according to GTEx (and the respective tissue) to each of the entries of this list. This seems to me like a common problem, but somehow I cannot find a "direct way" to do this. If I c ...
gwas snp eqtl gtex written 10 weeks ago by LNA10 • updated 8 weeks ago by alioniya0
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Comment: C: SNP enrichment, how to test for it?
... Could you briefly explain which approach finally worked for you? ...
written 5 months ago by LNA10
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Trait specific SNP prioritization
... Dear all, I am doing a GWAS for which I have only few samples available. According to the p-values I calculated using PLINK I don't have many significant signals. I would like to further investigate the SNPs with p-values in the "medium range" and now I am looking for a suitable prioritization tool ...
gwas prioritization snp enrichment written 5 months ago by LNA10
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How to include global MAF in GWAS analysis?
... Hi, I wonder if there is a possibility to use the global MAF for additional filtering of SNPs. I have a distribution of a quantitative trait for a few thousand people and SNP data for some individuals with extreme values. I was thinking that the effect allele should be highly enriched in the grou ...
gwas snp globalmaf written 12 months ago by LNA10
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Comment: C: GWAS with few samples
... I have to analyze that data. Since increasing the sample size is not an option, I want to know what is the best I can do? ...
written 12 months ago by LNA10
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GWAS with few samples
... Hello, I have SNP data of a Illumina HumanOmni5-4 BeadChip (4.2 million SNPs) for 28 samples with a quantitative trait. I have no experience doing GWAS studies and I need some advice. So far, I performed the quality control steps suggested by the GWASTools Vignette. Which testing procedure is be ...
gwas snp written 12 months ago by LNA10 • updated 12 months ago by coleman_jonathan330

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