User: sonia.olaechea

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Posts by sonia.olaechea

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Comment: C: gene ontology with reference list
... The output of both commands is the same: 17647 genes... Thank you anyway ;) ...
written 4 weeks ago by sonia.olaechea100
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Comment: C: gene ontology with reference list
... I used webtool Gene Ontology (GO):http://geneontology.org/ I only pasted my list on the webpage and it redirects me to PANTHER, where I can add my reference gene list. At this point it tells me that I have duplicate genes in my reference list... ...
written 4 weeks ago by sonia.olaechea100
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gene ontology with reference list
... Hi all, I would like to do an enrichment analysis/gene ontology analysis after an RNAseq differential expression analysis. For this, I would like to use a set of reference genes. I have already tried GO, but it's giving me some errors (it says that I have duplicate genes, while I've checked and I d ...
gene ontology rna-seq written 4 weeks ago by sonia.olaechea100 • updated 19 days ago by O'kin-10
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mitochondrial DNA in vcf for haplogrep2
... Hi everyone, I'm trying to analyse mitochondrial data from human samples, which I have stored in a `vcf`file. I've tried running `Haplogrep2` (both cmd and online) but my results do not make sense. Reading other posts, I've realised that I should first align my data to the `rCRS`sequence, so I was ...
vcf haplogrep2 mtdna written 10 weeks ago by sonia.olaechea100
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Manhattan plot with Bayes factor
... Hi everyone, I'm trying to do a Manhattan plot with my GWAS SNPs for which I've calculated Bayes factor. I've seen that people usually transform p-values with `-log10()`, but I would like to keep my Bayes factors untransformed. My problem is that I have values ranging from almost `0` to `10e^23` a ...
cmplot R qqman written 5 months ago by sonia.olaechea100
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Comment: C: extract genes and functions +/-50kb around a SNP
... I'd like to find the names of the genes that are 50kb up- and downstream of my list of `rs` and also their functions, pathways in which they are involved and their disease associations. ...
written 5 months ago by sonia.olaechea100
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Comment: C: extract genes and functions +/-50kb around a SNP
... Great, working! But... where can I find the list of tables from which to choose the information? ...
written 5 months ago by sonia.olaechea100
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Comment: C: extract genes and functions +/-50kb around a SNP
... Hi Pierre, I'm trying to use the mysql solution you proposed in your other post, but mysql gives me the following error: `ERROR 1146 (42S02) at line 2: Table 'hg19.snp130' doesn't exist`. Is this because I'm looking at a deprecated table? Is there maybe a more updated one for snp information? Thanks ...
written 5 months ago by sonia.olaechea100
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extract genes and functions +/-50kb around a SNP
... Hi everyone, I have a list of SNPs (`rs`) and I would like to extract all the genes and their functions that are located 50kb up- and downstream of them. I've been trying to generate the links to the corresponding pages of `UCSC` with Excel (which is more or less automatized). But I would like to ...
gwas snp written 5 months ago by sonia.olaechea100
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Comment: C: bayenv2: "initial epsilon zero or 1 locus 6912"
... Hi Katie, thank you very much for your answer! I asked the developpers of the bayenv2 and they told me that the problem was that the file contained SNPs with fixed allele frequencies (the same allele in all individuals, either 0 or 1). So I filtered my data by MAF 1% and the problems was solved. I ...
written 5 months ago by sonia.olaechea100

Latest awards to sonia.olaechea

Popular Question 10 weeks ago, created a question with more than 1,000 views. For 1000Genomes population allele frequencies for list of SNPs
Popular Question 4 months ago, created a question with more than 1,000 views. For Error: Line 2 of .ped file has more tokens than expected.
Popular Question 4 months ago, created a question with more than 1,000 views. For vcftools --TajimaD in sliding windows

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