Moderator: RamRS

gravatar for RamRS
RamRS19k
Reputation:
19,200
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Trusted
Location:
Houston, TX
Twitter:
@_RamRS
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Google Scholar Page
Last seen:
12 hours ago
Joined:
5 years, 4 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 • 4,089 results • page 1 of 409 • next >
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Comment: C: Bio.PDB parsing PDB file
... > I thought Bio.PDB was automatically set up to get files from the PDB database I don't think that's the case, you'll need to download the file first. Maybe Bio.PDB has a different method to download directly from PDB site, but it's not the `parser.get_structure()` method. > I have tried to ...
written 13 hours ago by RamRS19k
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Comment: C: What are the best tools/practices for CNV (structural variation) detection/analy
... We used XHMM for Whole Exome data. There is a step-by-step guide to get to CNV calls from BAM files [here][1]. Also, plink/seq has a cnv-denovo utility (I think that's what it's called) to detect de novo and transmitted CNVs. [This paper][2] should be useful. [1]: http://atgu.mgh.harvard.edu/xhmm/ ...
written 15 hours ago by RamRS19k
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Comment: C: Appending strings to fasta header from another file
... Hello Ming! Questions similar to yours can already be found at: How to match fasta header with the first column of a text file and append the second column of the text file to the end of the fasta header We have closed your question to allow us to keep similar content in the same thre ...
written 19 hours ago by RamRS19k
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Comment: C: Custom Database Has Spaces
... It could be that the DB was created with ncbi-blast from a pre-blast+ version and some quirk messes with header retrieval between versions. It's pretty mysterious, you may want to email NCBI with your findings. ...
written 20 hours ago by RamRS19k
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Comment: C: How to retrieve protein sequences from FASTA by using accession number?
... `Acc` seems to be an array so OP needs to account for that as well. ...
written 1 day ago by RamRS19k
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Comment: C: Software to predict impact of SNPs or Indels
... This is a professional forum run entirely by volunteers, and we need to strike a balance between being a pure knowledge repository and a Q&A forum. When a conversation meanders into personal preferences and repeated discussions on well-established practices, it needs to be discouraged. You're w ...
written 1 day ago by RamRS19k
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Comment: C: Software to predict impact of SNPs or Indels
... You're going in circles. The question has already been answered; there is no easier way to annotate a VCF. You should really read Kevin's comprehensive answer on the linked post, it along with jared.andrews07's comment on it and my answer here address everything you'll need. ...
written 1 day ago by RamRS19k
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Answer: C: Software to predict impact of SNPs or Indels
... From your question you seem to be really opinionated on SIFT. I think SIFT and PolyPhen2 are pretty standard and the way to go. Most sites allow you to upload a file, so you should be fine, unless you need to run more than the allowed volume, at which point you're better off using ANNOVAR. ...
written 1 day ago by RamRS19k
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Comment: C: Software to predict impact of SNPs or Indels
... Yes, you can bulk query against most of those. Most are available as VCF/BED files as they are essentially annotations tied to a chromosomal position. ...
written 1 day ago by RamRS19k
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Comment: C: I am new Here
... Hello nasitgasil123! We believe that this post does not fit the main topic of this site. Welcome to Biostars. I don't think it is necessary or advisable to announce your arrival with a dedicated post. For this reason we have closed your question. This allows us to keep the site focused on the to ...
written 1 day ago by RamRS19k

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