Moderator: RamRS

gravatar for RamRS
RamRS20k
Reputation:
20,280
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Trusted
Location:
Houston, TX
Twitter:
@_RamRS
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Google Scholar Page
Last seen:
5 hours ago
Joined:
5 years, 6 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 • 4,327 results • page 1 of 433 • next >
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Comment: C: haplotypeCaller groups comparison
... I cannot solve the scientific question for you, David. You can look at shared and exclusive variants between the two groups, but beyond that, it's all up to the questions you're asking. ...
written 5 hours ago by RamRS20k
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Answer: C: Using BCFtools to intersect multiple VCF files
... The command you're using translates to "pick variants found in any two files". You should change it so it follows a pattern similar to the fifth example in [the manual][1]: > Print a list of records which are present in A and B but not in C and D > ``` > bcftools isec -n~1100 -c all A.vcf ...
written 5 hours ago by RamRS20k
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Comment: C: haplotypeCaller groups comparison
... That's a warning, which can be ignored. GATK will stop if there's a serious ERROR. Wait for the VCF and examine it, it should be fine. ...
written 1 day ago by RamRS20k
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Comment: C: How to extract only sequences that contain a specific percentage of Cysteines (
... Sorry, we cannot "give you a little script". Please tell us what you've tried so far and where you're facing difficulties, and we can help you with specifics. ...
written 1 day ago by RamRS20k
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Comment: C: Error in CNV Calling with Annotation
... Welcome to Biostars and thank you for the contribution! 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 ...
written 1 day ago by RamRS20k
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Comment: C: Install trimmomatic on windows computer?
... Please do not add an answer unless you're answering the top-level question. Also, please avoid emoji like the tongue-out (`:p`) in a professional setting. ...
written 1 day ago by RamRS20k
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Comment: C: Only one hit per query on blastn?
... I think it does exactly what you need it to do. What it does not do is get you the "best" n hits. It gets you the first n hits, which may or may not be the best. See [this paper][1]: > A common strategy involves using the ‘-max_target_seqs’ parameter of the NCBI BLAST+ suite. According to the B ...
written 2 days ago by RamRS20k
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Comment: C: Counting number of base pairs and features in each bed file
... It's a tab separated file, you can simply pass the intersect result through awk and have it do `$3 - $2 +1` for the first file and `$7 - $6 + 1` for the second file, printing each sum out in a new column. ...
written 2 days ago by RamRS20k
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Comment: C: Counting number of base pairs and features in each bed file
... Can you give us a few sample lines of input and expected output? I don't understand what you mean by counting base pairs and features in a file that contains just contig names and coordinates. ...
written 2 days ago by RamRS20k
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Comment: C: Aligning using hg18
... >I assume this is because it is not annotated and indexed. It's not. It's because the parameter is being specified wrongly. I don't think STAR (or any unix tool for that matter) accepts an input file preceded by `--`. `--` is the prefix for long-form options, such as `--readFilesCommand`, which ...
written 2 days ago by RamRS20k

Latest awards to RamRS

Appreciated 2 days ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Commentator 2 days ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
Commentator 2 days ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: bash loop for alignment RNA-seq data
Scholar 15 days ago, created an answer that has been accepted. For A: "Update" Genotype fields from one VCF file to another
Commentator 21 days ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Benefit of platinum genomes in WGS experiment
Appreciated 5 weeks ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: bash loop for alignment RNA-seq data
Scholar 5 weeks ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
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Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: bash loop for alignment RNA-seq data
Scholar 7 weeks ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data
Scholar 8 weeks ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data
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Scholar 8 weeks ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data
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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: bash loop for alignment RNA-seq data
Scholar 10 weeks ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data

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