Moderator: Ram

gravatar for Ram
Ram17k
Reputation:
16,560
Status:
Trusted
Location:
Houston, TX
Twitter:
@_RamRS
Scholar ID:
Google Scholar Page
Last seen:
6 hours ago
Joined:
5 years 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 • 3,594 results • page 1 of 360 • next >
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Comment: C: Interpreting stats from gnomAD/ ExAC reference population
... >stats of various type of statistical information I'm sorry, what? >Could not find any open-source tool/ script online Have you tried R? ...
written 1 day ago by Ram17k
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Comment: C: Extract a list of SNPs from a BCF file
... >but I haven't had success What does that mean? What is the exact problem you're facing? Can you also paste the first few lines of your `mylist.txt` file? ...
written 1 day ago by Ram17k
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Comment: C: covert SAM to full length fasta
... Can you explain to us why you want a FASTA out of a BAM? BAM documents how reads (sequences with base-quality scores) align to a reference genome. BAM does not document in any way the changes one would need to make to the reference genome to get a consensus sequence. VCF files can be used to extract ...
written 1 day ago by Ram17k
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Comment: C: PLINK heterozygosity - Negative F statistic?
... Is this an answer to the top level question or a follow up question? ...
written 1 day ago by Ram17k
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Comment: C: Can I obtain data of individula's called variants from 1000 genome project?
... Hello mbk0asis! Questions similar to yours can already be found at: snps/indels with individual genotypes from 1000 genomes ftp site We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply belo ...
written 1 day ago by Ram17k
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Comment: C: Removing duplicate protein sequences from fasta file
... If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work. ![Upvote|Bookmark|Accept][1] [1]: https://image.ibb.co/dfsqrx/upvote_accept_bookmark.png ...
written 2 days ago by Ram17k
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Comment: C: Are cleavage sites always polyadenylated?
... Although you're looking to build a bioinformatics tool down the line, your current question is all biology and no computation. I think you'd have better luck at [Biology Stack Exchange](https://biology.stackexchange.com/) or [SeqAnswers](http://seqanswers.com/) ...
written 3 days ago by Ram17k
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Comment: C: PLINK genome file - understanding the output
... It's been 10 months, so the context has changed a LOT :-) I think I managed some sort of solution, but cannot recall what it was. ...
written 3 days ago by Ram17k
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Comment: C: Can two mates have different file size?
... File sizes can only be used as red flags when there is a significant difference in size, ~orders of magnitude, and even then the files need to share a lot of context to be compared. For example, if your mate files were 5G and 12G in size, there's probably something wrong. But if you have 2 BAM files ...
written 3 days ago by Ram17k
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Comment: C: Using Trinity for RNA-Seq analysis in model organisms
... AFAIK Trinity does assembly, not DE analysis. Have you looked at the actual DE tools that Trinity uses downstream (DESeq, edgeR, limma, voom etc?) ...
written 4 days ago by Ram17k

Latest awards to Ram

Appreciated 15 days ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Scholar 16 days ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: bash loop for alignment RNA-seq data
Scholar 18 days ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: bash loop for alignment RNA-seq data
Scholar 23 days ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: bash loop for alignment RNA-seq data
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: bash loop for alignment RNA-seq data
Scholar 25 days ago, created an answer that has been accepted. For A: bash loop for alignment RNA-seq data
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: calling the variants in a sample with respect to other sample
Popular Question 6 weeks ago, created a question with more than 1,000 views. For BLOSUM80 values differ - but what's the reason?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Problem using a custom blast database in tblastx
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Scholar 3 months ago, created an answer that has been accepted. For C: variant calling for more than 60 samples using haplotype caller
Scholar 3 months ago, created an answer that has been accepted. For A: How do I ask a question on Biostars?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How to extract all the mapped reads from bwa output
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