User: Ventrilocus

gravatar for Ventrilocus
Ventrilocus80
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80
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Location:
Netherlands, Rotterdam, ErasmusMC
Last seen:
11 hours ago
Joined:
6 months, 1 week ago
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b*****@hotmail.es

Posts by Ventrilocus

<prev • 12 results • page 1 of 2 • next >
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Answer: A: How many cells are represented in a sample going through NGS
... It is easy to compute. You just need the ng of DNA input in the NGS experiment. For example, assume we input 250 ng of DNA (that is what is required in a standard WGS experiment*). Each cell contains 6 pg of DNA, hence, the number of cells is: 250 ng * (1000 pg / 1 ng) * (1 cell / 6 pg**) = 41, ...
written 2 days ago by Ventrilocus80
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Answer: A: how to understand this "Jaccard distance" ?
... I think it is a reasonable metric. Just to be sure the details are clear: imagine you want to see how distant corona strain A is from corona strain B. First thing you do is sequence both strains, align them to the reference corona sequence and perform variant calling. Most of the sequence is identic ...
written 8 weeks ago by Ventrilocus80
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Answer: A: Ancient genome realignment?
... If you go to dbSNP (https://www.ncbi.nlm.nih.gov/snp/rs111670008), you may find the annotation of your SNP in both GRCh37/GRCh38. In your case: - GRCh37.p13 chr 4 NC_000004.11:g.89300101A>G (= chr4:89300101) - GRCh38.p12 chr 4 NC_000004.12:g.88378949A>G (= chr4:88378949) So, just check pos ...
written 8 weeks ago by Ventrilocus80
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Answer: A: Bismark methylation extract result interpretation
... Dear Devender, The region in your plot is of only 135 bp. No gene is that short. Make sure you have input the right genomic coordinates. ...
written 9 weeks ago by Ventrilocus80
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Comment: C: Windows installation of RNA Vienna Package
... Dear d.s.account, there are certainly clearer installation instructions for Linux. As a side note, it is not harder in Windows, simply different. You may be more successful via Virtualbox. However, its burdens entirely depend of what kind of use you have planned for these tools. If you require exte ...
written 5 months ago by Ventrilocus80
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Answer: A: Windows installation of RNA Vienna Package
... Dear d.s.account, *"The ViennaRNA Package consists of a C code library and **several stand-alone programs** for the prediction and comparison of RNA secondary structures".* You seem to have correctly installed a pre-compiled ViennaRNA package for a 64-bit windows machine. You need to know however, ...
written 5 months ago by Ventrilocus80
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Comment: C: Interpretation of results from ssizeRNA power analysis
... Dear Ana María, I do not know what is the best tool for your problem. A quick search in pubmed with "power calculation RNA-seq paired" grants: i) Power analysis for RNA-Seq differential expression studies using generalized linear mixed effects models Lianbo Yu, Soledad Fernandez & Guy Brock. ...
written 5 months ago by Ventrilocus80
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Answer: A: Interpretation of results from ssizeRNA power analysis
... Dear Ana María, if you go to the ssizeRNA_single help page, section "Value", you may read: *ssize*: sample sizes **(for each treatment)** at which desired power is first reached. This means that to achieve power of 80%, you would need 17 cases and 17 controls (also, that you reach a power of 94.9 ...
written 5 months ago by Ventrilocus80
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Comment: C: Variation in proportion of methylated CpGs between human cell types
... Dear Rubal, indeed, there seems to be a lower bound for global methylation. This is probably due to the involvement of DNA methylation in the repression of selfish elements in the genome (e.g. retrovirus, retrotransposons, etc) that conforms a large percentage of the human genome and hence a big co ...
written 6 months ago by Ventrilocus80
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Answer: A: Variation in proportion of methylated CpGs between human cell types
... Hi Rubal, the quick answer is that it depends on the tissue. If you compare **differentiated** blood cells with **differentiated** cells of the liver, you will probably see similar global methylation state. If you want to see higher differences in global methylation state, try employing WGBS data f ...
written 6 months ago by Ventrilocus80

Latest awards to Ventrilocus

Scholar 5 months ago, created an answer that has been accepted. For A: Variation in proportion of methylated CpGs between human cell types
Scholar 6 months ago, created an answer that has been accepted. For A: Variation in proportion of methylated CpGs between human cell types

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