User: vinayjrao

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vinayjrao180
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inStem, India
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Posts by vinayjrao

<prev • 146 results • page 1 of 15 • next >
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Comment: C: Create files in multiple directories via for loop
... Thank you both for your response. I am sorry that my problem was not very clear. I am working from the directory named `existing/`, which contains subdirectories such as `main/sub1/sub2/sub3/sub4/sub5/sub6/`. `sub6/` contains the file `data.tsv.bz2`. I wish to create a file called `sub1.txt` in the ...
written 1 day ago by vinayjrao180
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Create files in multiple directories via for loop
... Hi, I have around 500 directories, and I wish to first create an empty text file within each of these and then process my data files contained within sub-directories and redirect the output into the respective text files. An example of my existing folders - `exisiting/main/sub1/sub2/sub3/sub4/sub5/ ...
shell linux written 1 day ago by vinayjrao180
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Comment: C: Converting tsv into bam file
... I notice that, so what kind of file might this be? Should I try converting to `vcf` for annotation? ...
written 5 days ago by vinayjrao180
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Converting tsv into bam file
... Hi, We have obtained data from the European Genome-Phenome Archive, and the said data has been provided in `.tsv` format. In the summary of the dataset, they claim that this is a sequence file, so I am assuming that these could be indexed `bam` files. I would like to know whether there is a way to ...
genome R sequencing linux written 5 days ago by vinayjrao180 • updated 5 days ago by swbarnes29.2k
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Answer: C: How to login to dowload datasets from EGA - European Genome-phenome Archive?
... Thank you genomax, we wrote to them, and received a response saying that we need to use an updated version of the client, whose details can be fund [here][1] Edit: Could you please tell me how to close the post? [1]: https://ega-archive.org/download/downloader-quickguide-APIv3 ...
written 8 days ago by vinayjrao180
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How to login to dowload datasets from EGA - European Genome-phenome Archive?
... Hi, Recently my PI got an account on EBI-EGA, which we are able to login from the browser (Chrome and Safari), but when I tried logging into the account from the terminal (Ubuntu 20.04), I constantly receive errors - >java -jar EgaDemoClient.jar `Welcome to the EGA Secure Data Shell Demo.` `T ...
java written 8 days ago by vinayjrao180
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Appending output to a vector in R
... Hi, I am performing some calulations in a script, and would like to run a t-test on the outputs of both conditions. I would like to know if there is a way for me to tell R to run the script 'n' number of times (without a loop), and if I can append the output of the conditions (Control vs Treatment) ...
R written 8 weeks ago by vinayjrao180 • updated 8 weeks ago by antonioggsousa1.5k
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Comment: C: Annotating VCF files
... Thank you both for the suggestions. I will certainly try these options. ...
written 8 weeks ago by vinayjrao180
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Annotating VCF files
... Hi, I am working on whole exome sequencing data, and to annotate the resulting VCF files, I have been using wANNOVAR. However, we are now going to be receiving around 1000 unannotated VCF files from our collaborator, and the disadvantage of using wANNOVAR is that one can submit only two files at a ...
snp written 8 weeks ago by vinayjrao180
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Which of the output files of TrimGalore! must I align?
... Hello, I have been working on some whole exome sequencing data, and although I get the jist of the pipeline, in some of the samples I'm currently handling, I found adapter sequences, which were trimmed using TrimGalore! However, TrimGalore! generates to output files - `filename_trimmed.fq.gz` and ` ...
alignment snp sequencing written 12 weeks ago by vinayjrao180

Latest awards to vinayjrao

Scholar 7 days ago, created an answer that has been accepted. For C: How to login to dowload datasets from EGA - European Genome-phenome Archive?
Great Question 4 months ago, created a question with more than 5,000 views. For Interpreting GSEA enrichment plots/results
Epic Question 7 months ago, created a question with more than 10,000 views. For Setting the first row as column name in R
Popular Question 7 months ago, created a question with more than 1,000 views. For how to calculate fpkm?
Popular Question 7 months ago, created a question with more than 1,000 views. For Formula to calculate FPKM
Popular Question 7 months ago, created a question with more than 1,000 views. For BigWig to Wig Conversion
Popular Question 7 months ago, created a question with more than 1,000 views. For Interpreting GSEA enrichment plots/results
Great Question 7 months ago, created a question with more than 5,000 views. For grep a column based on a string
Popular Question 13 months ago, created a question with more than 1,000 views. For No differential gene expression after tuxedo protocol
Popular Question 13 months ago, created a question with more than 1,000 views. For Interpreting GSEA enrichment plots/results
Student 13 months ago, asked a question with at least 3 up-votes. For Interpreting GSEA enrichment plots/results
Popular Question 13 months ago, created a question with more than 1,000 views. For Formula to calculate FPKM
Popular Question 16 months ago, created a question with more than 1,000 views. For grep a column based on a string
Great Question 17 months ago, created a question with more than 5,000 views. For grep a column based on a string
Popular Question 18 months ago, created a question with more than 1,000 views. For Formula to calculate FPKM
Popular Question 19 months ago, created a question with more than 1,000 views. For Formula to calculate FPKM
Great Question 19 months ago, created a question with more than 5,000 views. For Setting the first row as column name in R
Popular Question 21 months ago, created a question with more than 1,000 views. For how to calculate fpkm?
Popular Question 22 months ago, created a question with more than 1,000 views. For Formula to calculate FPKM
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Formula to calculate FPKM
Popular Question 2.2 years ago, created a question with more than 1,000 views. For grep a column based on a string
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