User: iamakhilverma

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Posts by iamakhilverma

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Answer: A: Double normalization for DE
... One can't possibly get rid of all the biases in the data during RNA seq analysis, but depending on what kind of interpretations you desire, you can choose the experimental workflow and the normalization procedures to make the most out of your data(e.g *between-sample normalization* adjusts for effec ...
written 8 months ago by iamakhilverma0
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How to extract hypervariable region of mitochondrial dna from its fasta file?
... Recently I've done some analysis on mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed are linked to only hypervariable regions or not. To do that, I'll need to make new fasta files from the mit ...
genome gene sequence written 8 months ago by iamakhilverma0
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Topology file creation
... How can we use Charmm36 for creating a topology file for Polyoxometalates(Wells-Dawson structure)? ...
topology gromacs molecular dynamics written 9 months ago by iamakhilverma0
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How to integrate the transcriptomics data with kinetic metabolic models?
... I have created a convenience kinetics model. Now, I want to integrate the transcriptomic data with my convenience kinetics* model for altering/weighing the kinetic parameter values. I read some publications a bit similar to this work but couldn't get any proper idea of doing it in the right way. D ...
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Comment: C: Introduction to Structural Bioinformatics
... Any resource from where I can gap the theoretical bridge that I have to read the publications in this area. As I tried reading a couple of them but couldn't keep up with it. ...
written 13 months ago by iamakhilverma0
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Introduction to Structural Bioinformatics
... My undergraduate thesis is on the topic "Ligand design from protein-protein interfaces" and my PI has asked me to learn the basics of Structural bioinformatics over the summer so that I'll be able to start with my project as I begin my next semester(last week of July). Can someone please suggest me ...
structural bioinformatics protein written 13 months ago by iamakhilverma0 • updated 13 months ago by Jean-Karim Heriche23k
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Comment: C: How can I run a same command in mac terminal for multiple files in a folder?
... It's creating only 1 output file. (actually, it's rewriting the same output file for every input file) ...
written 2.2 years ago by iamakhilverma0
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Comment: C: How can I run a same command in mac terminal for multiple files in a folder?
... Mouse genome. And RAM isn't the problem. I've got a RAM 64 GB desktop(Mac, currently using) and 192 GB RAM Workstation Dell. ...
written 2.2 years ago by iamakhilverma0
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How can I run a same command in mac terminal for multiple files in a folder?
... How can I run the same command in mac terminal for multiple files in a folder? The files are named like `24538_7#1_paired1.fq`, `24538_7#1_paired2.fq`, `24538_7#2_paired1.fq`, `24538_7#2_paired2.fq`, `24538_7#3_paired1.fq`, `24538_7#3_paired2.fq`, and so on. The command is: STAR --runThreadN 1 ...
alignment rna-seq sequencing written 2.2 years ago by iamakhilverma0 • updated 2.2 years ago by genomax87k

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