User: vinayjrao
vinayjrao • 180
- Reputation:
- 180
- Status:
- Trusted
- Location:
- inStem, India
- Last seen:
- 1 day, 6 hours ago
- Joined:
- 3 years, 6 months ago
- Email:
- v********@gmail.com
Posts by vinayjrao
<prev
• 146 results •
page 1 of 15 •
next >
0
votes
0
answers
70
views
0
answers
... 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
vinayjrao • 180
2
votes
0
answers
70
views
0
answers
... 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/ ...
written 1 day ago by
vinayjrao • 180
0
votes
1
answer
65
views
1
answers
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
vinayjrao • 180
1
vote
1
answer
65
views
1
answer
... 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 ...
1
vote
1
answer
60
views
1
answers
... 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
vinayjrao • 180
3
votes
1
answer
60
views
1
answer
... 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 ...
written 8 days ago by
vinayjrao • 180
1
vote
1
answer
115
views
1
answer
... 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) ...
written 8 weeks ago by
vinayjrao • 180
• updated
8 weeks ago by
antonioggsousa • 1.5k
0
votes
0
answers
160
views
0
answers
Comment:
C: Annotating VCF files
... Thank you both for the suggestions. I will certainly try these options. ...
written 8 weeks ago by
vinayjrao • 180
0
votes
0
answers
160
views
0
answers
... 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 ...
written 8 weeks ago by
vinayjrao • 180
0
votes
0
answers
128
views
0
answers
... 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 ` ...
written 12 weeks ago by
vinayjrao • 180
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
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For understanding bedtools coverage output
Centurion
2.4 years ago,
created 100 posts.
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For understanding bedtools coverage output
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For Ballgown Error in file(file, "rt") : invalid 'description' argument
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1427 users visited in the last hour