User: omg what am I doing

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Posts by omg what am I doing

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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 9 weeks ago by omg what am I doing60
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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 10 weeks ago by omg what am I doing60
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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 10 weeks ago by omg what am I doing60
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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 3 months ago by omg what am I doing60
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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 ...
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Answer: A: Merge VCFs with overlapping samples
... You need bcftools concat, I used the command below and got the result you described. bcftools concat -a filtered_indels_annotated.vcf.gz filtered_snps_annotated.vcf.gz -Ov -o filtered_BC_merged.vcf Some useful info here on the -a option: https://samtools.github.io/bcftools/bcftools.html#norm ...
written 4 months ago by omg what am I doing60

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