Moderator: Ram

gravatar for Ram
Ram13k
Reputation:
12,790
Status:
Trusted
Location:
New York
Twitter:
@_RamRS
Scholar ID:
Google Scholar Page
Last seen:
3 hours ago
Joined:
4 years, 7 months ago
Email:
r****@nyu.edu

Bioinformatician turned Microsoft technologies developer turned bioinformatician. I love messing with text. UNIX>R>Python>Perl programmer, Excel pro, master Googler, database expert. 

I'm an amateur biologist interested in translational human genetics and healthcare.

Twitter: @_ramrs

Posts by Ram

<prev • 2,826 results • page 1 of 283 • next >
0
votes
3
answers
142
views
3
answers
Comment: C: Replacing the Chr names and position notions in vcf
... Please try not to use "dear", it sounds inappropriate in a professional scientific forum. Thank you! ...
written 8 hours ago by Ram13k
0
votes
0
answers
99
views
0
answers
Comment: C: how to find snps among samples
... You're telling me the *what*, I'm asking you about the *why*. Have you discussed with your client why they want to do this (their ultimate aim, as I mentioned earlier)? Unless this is common practice in plant bioinformatics, I do not think this approach makes sense. ...
written 1 day ago by Ram13k
0
votes
0
answers
103
views
0
answers
Comment: C: How to run PLINK from a personal computer
... Check WouterDeCoster's comment: https://www.biostars.org/p/299211/#299293 ...
written 2 days ago by Ram13k
0
votes
0
answers
103
views
0
answers
Comment: C: How to run PLINK from a personal computer
... > cant run any command because it says: it is not recognized as an internal or external command This usually means that the executable that you're trying to run is not in your `PATH`. Ensure you've added the directory in which the executable it to your `PATH`. ...
written 2 days ago by Ram13k
0
votes
0
answers
83
views
0
answers
Comment: C: How to bechmark a human dataset ? (is it needed)
... Based on your past questions, IMO you’re obsessing over TP/FP a lot. Run preliminary QC, extract variants of significance/interest and invest effort in in-depth QCing them. ...
written 2 days ago by Ram13k
0
votes
3
answers
142
views
3
answers
Comment: C: Replacing the Chr names and position notions in vcf
... I don’t think we should be providing code - how would OP learn if the solution is ready-made for them? ...
written 2 days ago by Ram13k
0
votes
3
answers
142
views
3
answers
Answer: A: Replacing the Chr names and position notions in vcf
... Create a file with 2 columns - the `gi|` notation and the notation you want. Read the above file to a dictionary. Then, read the VCF file in a streaming fashion and substitute each occurrence of the old notation with the new one. This is the strategy. I'd recommend you coding this yourself so you ...
written 2 days ago by Ram13k
1
vote
0
answers
107
views
0
answers
Comment: C: Sorting file by column, with missing values
... You'd need to `head -2 && tail -n +3 | sort ...` to sort properly. That header is super unwieldy. ...
written 3 days ago by Ram13k
0
votes
0
answers
79
views
0
answers
Comment: C: Getting Haplotypes from a VCF file
... Unfortunately, no. Maybe if you could explain the purpose behind this exercise, we could get some clarity. ...
written 3 days ago by Ram13k
0
votes
0
answers
79
views
0
answers
Comment: C: Getting Haplotypes from a VCF file
... Almost. I've corrected it so it's better. You can use the formatting bar (especially the `code` option) to present your post better. ![Formatting bar][1] [1]: http://i66.tinypic.com/33kdnjt.png ...
written 4 days ago by Ram13k

Latest awards to Ram

Scholar 14 days ago, created an answer that has been accepted. For A: BCFtools variant calling format
Commentator 19 days ago, created a comment with at least 3 up-votes. For C: Cuffdiff input error
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: why aren't relational DB's used more for genomic data?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: why aren't relational DB's used more for genomic data?
Scholar 10 weeks ago, created an answer that has been accepted. For A: BCFtools variant calling format
Appreciated 3 months ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Scholar 3 months ago, created an answer that has been accepted. For A: BCFtools variant calling format
Scholar 3 months ago, created an answer that has been accepted. For A: Recompile bedops with increased TOKENS_MAX_LENGTH
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Cuffdiff input error
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Cuffdiff input error
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Cuffdiff input error
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: bash loop for alignment RNA-seq data
Scholar 8 months ago, created an answer that has been accepted. For A: Problem using a custom blast database in tblastx
Appreciated 8 months ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Appreciated 8 months ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
Scholar 9 months ago, created an answer that has been accepted. For A: Problem using a custom blast database in tblastx
Scholar 9 months ago, created an answer that has been accepted. For A: Problem using a custom blast database in tblastx
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
Appreciated 11 months ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 781 users visited in the last hour