User: Ventrilocus

gravatar for Ventrilocus
Ventrilocus50
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50
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Trusted
Location:
Netherlands, Rotterdam, ErasmusMC
Last seen:
2 days, 9 hours ago
Joined:
1 month ago
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b*****@hotmail.es

Posts by Ventrilocus

<prev • 8 results • page 1 of 1 • next >
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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 days ago by Ventrilocus50
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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 6 days ago by Ventrilocus50
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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 8 days ago by Ventrilocus50
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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 11 days ago by Ventrilocus50
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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 22 days ago by Ventrilocus50
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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 26 days ago by Ventrilocus50
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Answer: A: Help required to understand Hi-C data and it's Usage
... Hi rohitsatyam102, it is quite simple. You first need to understand the HiC-protocol Initial conditions: Distant sequences form 3D loop structures, stabilized by proteins. 1. Cross-linking: Protein-DNA interactions are fixed. 2. Intra-molecular ligation: distant sequences are joined together ...
written 26 days ago by Ventrilocus50
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Answer: A: Repetitive motifs on Illumina 450k derived sequences
... Dear gbayon, what you are seeing here is probably the sums of two biases: 1) Given: i) bisulfite conversion, ii) whole genome amplification and iii) 450K may target plus or minus strand: plus strand C's become T's and minus strand G's become A's. As a result, you face reduced complexity: plus stra ...
written 4 weeks ago by Ventrilocus50

Latest awards to Ventrilocus

Scholar 11 days ago, created an answer that has been accepted. For A: Variation in proportion of methylated CpGs between human cell types
Scholar 26 days ago, created an answer that has been accepted. For A: Variation in proportion of methylated CpGs between human cell types

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