User: vinayjrao

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vinayjrao170
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JNCASR, India
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Posts by vinayjrao

<prev • 133 results • page 1 of 14 • next >
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Filtering wANNOVAR output on terminal
... Hi, I am working on some whole exome data, which were annotated using the web based ANNOVAR (wANNOVAR). I downloaded the `.csv` output. When I open the file with Excel, a) my laptop slows down quite a lot, and b) there are a lot of columns, which lead to making errors at times. Below is a sample of ...
snp written 2 days ago by vinayjrao170
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What type of duplicates are to be removed while analyzing whole exome data?
... Hi, I am analyzing whole exome data to analyze InDels and SNPs between healthy control and diseased patients. Since I'm new to analyzing exome data, I would like to know whether I should remove all duplicates or only sequencing duplicates, because removing all duplicates can also result in neglecti ...
exome-seq snp written 3 days ago by vinayjrao170
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Comment: C: Correlation between coverage and variant calling
... Thank you both for the insight. Although, it is still not clear to me whether a decrease in fastq file size will linearly reduce the number of variants? ...
written 4 months ago by vinayjrao170
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Correlation between coverage and variant calling
... Hi, I analyzed a few human Exome-Seq data sets, and I noticed that their fastq files were around 2.5 Gb each. I am analyzing another set, where the fastq files are around 900 Mb. After aligning both with hg38, and following the same pipeline, I noticed upon variant calling (GATK HaplotypeCaller) th ...
exome-seq variant_calling snp written 4 months ago by vinayjrao170 • updated 4 months ago by harish290
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Filtering 2-fold differentially expressed genes
... Hi, I am working with a microarray dataset, which is in the format - > Control      Control2      Treatment      Treatment2 The dataset has been log transformed. I want to know if there a way to filter the data such that I get genes whose fold difference is greater than 2 fold in Treatment as ...
R microarray written 12 months ago by vinayjrao170 • updated 12 months ago by Nicolas Rosewick8.8k
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Comment: C: Averaging multiple columns
... Thank you for your help. It works perfectly. ...
written 12 months ago by vinayjrao170
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Comment: C: Averaging multiple columns
... Thank you for your reply. I am still working on it. Will update once done. ...
written 12 months ago by vinayjrao170
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Averaging multiple columns
... Hi, I have a file with five columns, from which I want the mean of the last four columns where the first rows of the first column are the same. For example, my file looks like this - A 1 1 1 1 A 1 3 1 1 A 1 1 2 3 B 5 7 2 4 C 2 1 5 1 C 2 2 3 6 The desired output is - A ...
R shell written 12 months ago by vinayjrao170 • updated 12 months ago by zx87549.3k
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How to merge 2 dataframes based on common column names?
... Hi, I have two data frames, both containing the columns `GeneName` and `logFC`. Using `intersect()`, I have obtained the common genes between the two. I want to know how to merge my two dataframes based on the common dataframe. Thank you. ...
R written 12 months ago by vinayjrao170 • updated 12 months ago by lakhujanivijay5.0k
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Comment: C: Probe Sequence Missing from Agilent Data
... Thanks Kevin, for the clarification. Although, I would like to know why I should remove these after normalization, and what is the significance of these positive control probes? ...
written 12 months ago by vinayjrao170

Latest awards to vinayjrao

Epic Question 10 weeks ago, created a question with more than 10,000 views. For Setting the first row as column name in R
Popular Question 10 weeks ago, created a question with more than 1,000 views. For how to calculate fpkm?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Formula to calculate FPKM
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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Interpreting GSEA enrichment plots/results
Great Question 10 weeks ago, created a question with more than 5,000 views. For grep a column based on a string
Popular Question 8 months ago, created a question with more than 1,000 views. For No differential gene expression after tuxedo protocol
Popular Question 8 months ago, created a question with more than 1,000 views. For Interpreting GSEA enrichment plots/results
Popular Question 8 months ago, created a question with more than 1,000 views. For Formula to calculate FPKM
Student 8 months ago, asked a question with at least 3 up-votes. For Interpreting GSEA enrichment plots/results
Popular Question 11 months ago, created a question with more than 1,000 views. For grep a column based on a string
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Popular Question 13 months ago, created a question with more than 1,000 views. For Formula to calculate FPKM
Great Question 14 months ago, created a question with more than 5,000 views. For Setting the first row as column name in R
Popular Question 14 months ago, created a question with more than 1,000 views. For Formula to calculate FPKM
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