Moderator: RamRS

gravatar for RamRS
RamRS25k
Reputation:
25,420
Status:
Trusted
Location:
Houston, TX
Twitter:
@_RamRS
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
6 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.

Posts by RamRS

<prev • 5,440 results • page 1 of 544 • next >
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Comment: C: Merging bed bim fam files from chromosome 1 to 22 at one time
... What is in there that justifies your `rm` command? ...
written 3 hours ago by RamRS25k
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Comment: C: Merging bed bim fam files from chromosome 1 to 22 at one time
... Why the `rm`? OP's commands do not show an existing file by that name. ...
written 3 hours ago by RamRS25k
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Comment: C: Downstream RNA seq analysis
... I think one way to go would be to do a gene set enrichment analysis to look for pathways (or GO terms) where component genes are over-represented. This would help translate a set of genes to have some sort of biological meaning. ...
written 6 hours ago by RamRS25k
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Comment: C: Pipeline for exome sequencing
... This is a bunch of links and sample commands, not a pipeline. ...
written 1 day ago by RamRS25k
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Comment: C: How to pass arguments in a bash script to perform read alignment to the referenc
... I built a bash-based pipeline for exome sequencing a couple of years ago. From your script above, I gather that your shell experience is quite basic and nowhere close enough to be able to build a robust pipeline that accounts for various edge cases. Please invest time in learning a workflow manager, ...
written 1 day ago by RamRS25k
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Comment: C: How to pass arguments in a bash script to perform read alignment to the referenc
... > You've given that script admin privileges No, OP has changed permissions using a `sudo` command, which is meaningless in this context if OP owns the script file. > You may have treated the symptom of your script failing, but not the cause. OP has treated neither. OP is not running `sudo s ...
written 1 day ago by RamRS25k
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Comment: C: Biopython gives ValueError: Sequences must all be the same length even though se
... Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (`text` becomes `text`), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time. ...
written 1 day ago by RamRS25k
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Comment: C: Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
... As an aside, are you sure a BED file would even work? I recall running into an issue a few years ago where GATK needed an `interval_list` file, which was similar but not identical to the BED format. ...
written 1 day ago by RamRS25k
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Comment: C: Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
... Just my 2 cents: I'm using the `*_Padded` file to subset my VCF file. Be aware that the regions can overlap. ...
written 2 days ago by RamRS25k
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Comment: C: Issues installing new VEP: Bio::DB:HTS library not found
... When you have an update, please add it as a reply in the appropriate spot. Do not edit your question unless it is missing some information it should have contained at the time of creation. ...
written 2 days ago by RamRS25k

Latest awards to RamRS

Popular Question 26 days ago, created a question with more than 1,000 views. For Meta: Should accepting your own answers multiple times get you points each time?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Meta: Should accepting your own answers multiple times get you points each time?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Meta: Should accepting your own answers multiple times get you points each time?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Where can I download the blast version that includes formatdb ?
Scholar 7 weeks ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Scholar 7 weeks ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: .slurm vs .sh files
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Bioinformatics and biotechnology market in future.
Scholar 9 weeks ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For C: .slurm vs .sh files
Scholar 10 weeks ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Scholar 10 weeks ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Scholar 11 weeks ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: .slurm vs .sh files
Scholar 11 weeks ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Where can I download the blast version that includes formatdb ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: .slurm vs .sh files
Scholar 4 months ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Scholar 4 months ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Scholar 4 months ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics and biotechnology market in future.

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