User: vijay

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vijay1.4k
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Posts by vijay

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Differential expression analysis of transcriptome data
... Thanks for your response. Please can you let me know if explaining differential expression only based on log(FPKM) values will make sense. In other words, is that technically correct and acceptable for publication? ...
written 2.8 years ago by vijay1.4k
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Differential expression analysis of transcriptome data
... Dear Folks, I am currently working on brain transcriptome data of a male and female fish obtained using RNASeq. I wish to compare them and obtain the differentially expressed genes. All that I have got is a table containing the Transcripts per milllion (TPM) and the FPKM value for both the samples. ...
deseq rna-seq transcriptome written 2.8 years ago by vijay1.4k • updated 2.8 years ago by Thibault D.510
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Comment: C: Error while running ktreedist
... Hello vijay! We believe that this post does not fit the main topic of this site. This issue has been sorted out!! Thanks!! For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in ...
written 3.4 years ago by vijay1.4k
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(Closed) Error while running ktreedist
... Dear all, I am attempting to determine the Robinson–Foulds metric between a pair of trees using ktreedist. Unfortunately, I am encountering the below error while running the program. ERROR (species - tips):The tips of tree '1' in './tree1.nwk' are different to those of reference tree. I have veri ...
treedist written 3.4 years ago by vijay1.4k
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Comment: C: Reading Uparse Output In Mothur
... Hi Josh, I was able to generate rarefaction curves using the standard protocols suggested by mothur. I understand that mothur requires a .list or a .rabund file to create a rarefaction file. I had a try at UParse and I got an OTU table from it. I was just curious to know how do I convert this clu ...
written 5.0 years ago by vijay1.4k
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Reading Uparse Output In Mothur
... Dear All, Can someone suggest me on how to generate a rarefaction curve in mothur using the cluster output from Uparse.? Cheers, Vijay ...
written 5.0 years ago by vijay1.4k
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Comment: C: Do You Feel Good Or Bad About Putting Your Photo At Biostar?
... I am facing this issue as well!! someone pls let us know. ...
written 5.0 years ago by vijay1.4k
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Comment: C: Molecular Dynamics Simulation
... I would rather suggest you to revisit the causes for the failure. Take a look at the solvent models that you have chosen(if any), the time step you have set, the initial and periodic boundary conditions and other parameters of course. Unless you have a strong theoretical data behind the interactions ...
written 5.0 years ago by vijay1.4k
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Comment: C: Why Does Mothur Require An Alignment Step Before Clustering?
... Thanks for your response Istvan. I am able to understand that. But my point is , the number of OTU's that are generated vary between QIIME and MOTHUR for the same dataset at 97%. So I am skeptic if the alignment against a silva reference that is done in mothur causes this change. ...
written 5.0 years ago by vijay1.4k
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Answer: A: Molecular Dynamics Simulation
... I think its all about the results that you come up matters the most than the software package that you use. Comparison of packages is fine, but MD simulations are computationally intensive, hence it is better to proceed with single package, but definitely with concrete base data. Dynamics can vary t ...
written 5.0 years ago by vijay1.4k

Latest awards to vijay

Popular Question 6 months ago, created a question with more than 1,000 views. For Differential expression analysis of transcriptome data
Popular Question 10 months ago, created a question with more than 1,000 views. For Predicted Relative Metabolomic Turnover (Prmt):
Great Question 13 months ago, created a question with more than 5,000 views. For Assembly Illumina Paired End Reads
Great Question 13 months ago, created a question with more than 5,000 views. For Why Does Mothur Require An Alignment Step Before Clustering?
Great Question 13 months ago, created a question with more than 5,000 views. For Tools For Metagenomic Data Analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For Predicted Relative Metabolomic Turnover (Prmt):
Great Question 17 months ago, created a question with more than 5,000 views. For Assembly Illumina Paired End Reads
Popular Question 17 months ago, created a question with more than 1,000 views. For Predicted Relative Metabolomic Turnover (Prmt):
Popular Question 21 months ago, created a question with more than 1,000 views. For Adding New Atom To Parameter File In Autodock
Great Question 2.4 years ago, created a question with more than 5,000 views. For Tools For Metagenomic Data Analysis
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Adding New Atom To Parameter File In Autodock
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Evaluation Of Protein Model Based On Homology Modelling
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Adding New Atom To Parameter File In Autodock
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Assembly Illumina Paired End Reads
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Why Does Mothur Require An Alignment Step Before Clustering?
Student 2.6 years ago, asked a question with at least 3 up-votes. For Why Does Mothur Require An Alignment Step Before Clustering?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Assembly Illumina Paired End Reads
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Popular Question 2.8 years ago, created a question with more than 1,000 views. For Error When Using Makeblastdb On A Large File
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Gold Standard 3.5 years ago, created a post with more than 25 bookmarks. For Tools For Metagenomic Data Analysis
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Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: How To Learn To Build A Bioinformatics Oriented Web Site
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Assembly Illumina Paired End Reads
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