User: nick

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nick100
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Posts by nick

<prev • 23 results • page 1 of 3 • next >
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Comment: C: WGCNA analysis for bisulfite data.
... Did you use `bismark_methylation_extractor`? I see from the [user guide](https://rawgit.com/FelixKrueger/Bismark/master/Docs/Bismark_User_Guide.html#appendix-iii-bismark-methylation-extractor) that the `--bedGraph` flag will output what you need. I inaccurately implied that bismark will create a ma ...
written 11 weeks ago by nick100
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Comment: C: Interpretation of Beta values : Methylation data
... Not 10% percent of your samples but 10% of cells in your sample for that site. ...
written 11 weeks ago by nick100
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Answer: A: Beta values for hyper- and hypo- methylated probes
... I think you are mixing different concepts. Methylated and unmethylated generally refer to single sites. When you examine a bulk of cells, the beta values represent the fraction of alleles that are methylated. If you get beta=1 for a given site you know that site is always methylated in that gruop o ...
written 11 weeks ago by nick100
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Comment: C: WGCNA analysis for bisulfite data.
... I haven't done this kind of analysis myself, but bisulphite *sequencing* data consist of reads. You must align the reads and analyze them with tools such as [bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/). At the end of the process you will obtain a matrix of Beta-scores (repre ...
written 11 weeks ago by nick100
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Answer: A: How to deside gene CNVs from .cnr outputs
... To merge bins you need to run `cnvkit.py segment` to create `.cns` files. Assuming a diploid genome: - Log2(CR) = -1 → CR = 0.5 → 1 copy (of a segment/gene). - Log2(CR) = 0 → CR = 1 → copies - Log2(CR) = +1 → = 2 → 4 copies - Log2(CR) = 0.58 → = 1.5 → copies Of course you have to consider a bit o ...
written 7 months ago by nick100
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Comment: C: confused about how to run pipeline
... I think there's an error in the documentation because it shows that you have to pass an access file but first you need to run `cnvkit.py access` to create it. Do what Paul suggests in his answer. ...
written 7 months ago by nick100
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Comment: C: How To Compare Gene Expression And Methylation Level Of A Gene
... As suggested in Neilfws's comment I decided to choose the probe with the highest variance. ...
written 10 months ago by nick100
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Biopython pairwise2 alignment: is one_alignment the best alignment?
... I started using `pairwise2.align` function from [Biopyton][1] with the `one_alignment` set to True. I was wondering if that single alignment returned is the best one. With Smith-Waterman it should be but I'm not sure if that's what's been implemented. [1]: https://github.com/biopython/biopython/b ...
alignment biopython written 16 months ago by nick100 • updated 16 months ago by rayoub110
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Comment: C: TCGA & METABRIC Breast Cancer Subtype Survival Curve
... [here][1] or using R package TCGAbiolinks [1]: https://portal.gdc.cancer.gov/ ...
written 22 months ago by nick100
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Answer: A: TCGAquery function from TCGAbiolinks
... Have you tried with`GDCquery`? ...
written 2.0 years ago by nick100

Latest awards to nick

Popular Question 5 months ago, created a question with more than 1,000 views. For DNA methylation analysis with RnBeads: start analysis from Beta-values
Appreciated 10 months ago, created a post with more than 5 votes. For How To Compare Gene Expression And Methylation Level Of A Gene
Popular Question 16 months ago, created a question with more than 1,000 views. For DNA methylation analysis with RnBeads: start analysis from Beta-values
Popular Question 22 months ago, created a question with more than 1,000 views. For abyss-fac: command not found on Kubuntu 14.04
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Tcga Data From Synapse: Whitelisting Criteria
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How To Compare Gene Expression And Methylation Level Of A Gene
Student 5.3 years ago, asked a question with at least 3 up-votes. For How To Compare Gene Expression And Methylation Level Of A Gene

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