User: ReWeeda

gravatar for ReWeeda
ReWeeda50
Reputation:
50
Status:
New User
Location:
University of Bologna
Last seen:
13 hours ago
Joined:
3 years, 5 months ago
Email:
d**************@gmail.com

I'm an italian Phd student in "Data Science and Computation" with a background in Biotechnologies and Bioinformatics.

Posts by ReWeeda

<prev • 12 results • page 1 of 2 • next >
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Comment: C: copywriteR CNV identification
... I can suggest you to take into consideration the number of reads mapped to a segment if you have enough samples. Using dummy numbers: Suppose that the number of mapped reads in segment A spans between 10 and 30 for normal and tumor while the number of mapped reads for segment B spans between 1000 an ...
written 6 months ago by ReWeeda50
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Answer: A: Whole Exome CNV tools
... Hi BAGeno! There are plenty of tools out there for CNVs detection from WES data! In addition to VarScan, cited by 2nelly, you can also try with: - [Sequenza][1] - [XCAVATOR][2] - [ADTEX][3] - [iCNV][4] - [CONTRA][5] - [FREEC][6] - [CNVkit][7] I also suggest you to read [this][8] article. ...
written 6 months ago by ReWeeda50
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Answer: A: copywriteR CNV identification
... Well, `2^(Log2Ratio)` doesn't give the number of copy. Reversing the logarithm gives you the original ratio between sample and control. Taking the first line of the output you provided, reversing the log2ratio you can find that the sample has got a number of copies in that region that's about 0.89 ...
written 6 months ago by ReWeeda50
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Answer: A: [Clustal Omega] Posterior Probability Output File; columns meaning
... If someone ever need in the future: the answer has been given to me by the "help desk" of Clustal developers. Column 5: It's the sum of the probabilities of each residue of being aligned to its corresponding position in the HMM computed when the `--posterior-out=` option is flagged Column 6: Is t ...
written 19 months ago by ReWeeda50
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[Clustal Omega] Posterior Probability Output File; columns meaning
... Hi! Just to introduce the context: I clustered protein structures given annotated function and architectures (structural domains along the sequence) and now I want to perform a MSA for each cluster trying to highlight emergent relations at sequence level. I'm trying different softwares (mafft, cl ...
msa posterior probability clustal omega written 19 months ago by ReWeeda50
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Answer: A: Formatting problem gene table conversion
... Alternatively, if you are not familiar with awk, you can use a simple script like the following one written in python: with open('file_name_or_path_here','r') as file_: for line in file_: line=line.rstrip() if line[0]=='>': gene = line else: ...
written 20 months ago by ReWeeda50
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Comment: C: [ Mustang ] Problem with Server
... I've run mustang over 2 structures and I've also tried specifying directly through the command path and structures. In both case everything was completed fine and correctly. I'm not able to explain why, I've applied the same procedure. ...
written 3.4 years ago by ReWeeda50
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Comment: C: [ Mustang ] Problem with Server
... No, nothing called ''core'' ...
written 3.4 years ago by ReWeeda50
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[ Mustang ] Problem with Server
... Good Morning, working on a personal project I've recently obtained the accession to a server in order to run Multiple Structural Alignment process on it instead of using my pc that I require for studying (I'm a student). So, I use MUSTANG to compute the multiple structural alignment over a set of ...
server mustang written 3.4 years ago by ReWeeda50
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Comment: C: How to edit .PDB files fast ?
... you're right. Nevertheless I've adopted another solution merging different ideas retrieved on the web. Now I've just to write a shell script to run my .py over all the structures with just one click. ...
written 3.4 years ago by ReWeeda50

Latest awards to ReWeeda

Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to edit .PDB files fast ?

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