User: omg what am I doing

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Posts by omg what am I doing

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Comment: C: How To Merge Two Fastq.Gz Files?
... I followed this and just used `cat` to combine my .fastq.gz files. For anyone else, make sure you use `zcat` and not just `cat` to combine gzipped files. `zcat` decompresses first, `cat` does not. If you combine gzipped fastq files with just `cat`, you will get gibberish downstream. ...
written 11 weeks ago by omg what am I doing70
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... So I have some (probably hispanic descent) tumor WGS samples in red dots on my PCA plot projected onto 1kg data like in this tutorial (btw thank you Kevin Blighe for pointing me to this tutorial), and I am wondering how closely can we expect unknown samples to follow any given 1kg clusters. My red d ...
written 3 months ago by omg what am I doing70
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Comment: C: Does the GENOtation web-based PCA tool work?
... Thank you Kevin I will try your workflow ...
written 3 months ago by omg what am I doing70
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Does the GENOtation web-based PCA tool work?
... http://genotation.stanford.edu/#PCA I was trying to get a nice PCA visual of some of samples on top of Hapmap data using the web-based Genotation tool from Stanford linked above. I converted my VCF into the 23andMe format like they asked, but no matter what samples I seem to enter into the tool, th ...
wgs pca genotation snp stanford written 4 months ago by omg what am I doing70 • updated 4 months ago by Kevin Blighe63k
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Comment: C: Noisy germline CNV data using CNVKit
... thank you so much for the help ...
written 4 months ago by omg what am I doing70
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Comment: C: CNVKit scatter graph will not plot individual chromosomes
... Yes, seems to work fine with the chromosome bounds specified. ...
written 14 months ago by omg what am I doing70
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Comment: C: CNVKit scatter graph will not plot individual chromosomes
... Thank you, I forgot I had removed the chr prefixes in my analysis. That resolved the error but I got a different error IndexError: indices are out-of-bounds Apparently this was an issue that was fixed in 0.9.6 according to this thread [https://www.biostars.org/p/326154/][1] but it still showed ...
written 14 months ago by omg what am I doing70
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CNVKit scatter graph will not plot individual chromosomes
... Hello, I am running CNVKit 0.9.6 and I cannot get the scatter function to plot an individual chromosome. It will generate a PNG of all chromosomes but I cannot display just one using: cnvkit.py scatter 27s.cnr -s 27s.calls.cns -c chr9 -o 27s_scatter_chr9.png I get an error: ValueError: ...
cnvkit.py cnvkit cnv cnvkit.py scatter written 14 months ago by omg what am I doing70
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Answer: A: How to know if high expression of a gene is really a good independent marker for
... I would approach it by thinking about what is known about the function of the gene already...is it a known regulator of an established tumor suppressor or oncogene? A KEGG search might help with that (to follow Kevin's example here is p53 https://www.kegg.jp/kegg-bin/show_pathway?ko04110+K04451). If ...
written 15 months ago by omg what am I doing70
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Noisy germline CNV data using CNVKit
... **Context:** I'm a new CNVKit user (using 0.9.6). I have 6 exome-seq samples (from saliva DNA) that I want to do germline copy number calling on. 2 of the samples are from saliva of healthy individuals and the other 4 are from saliva of individuals with breast cancer, all in the same extended family ...
cnvkit copy number variation germline cnv gcnv written 15 months ago by omg what am I doing70 • updated 5 months ago by sutturka170

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