User: drautuna

gravatar for drautuna
drautuna60
Reputation:
60
Status:
New User
Location:
United States
Last seen:
1 year, 5 months ago
Joined:
4 years, 8 months ago
Email:
d*******@g.ucla.edu

Posts by drautuna

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Annovar: how to update sequence length based on deletion size
... Hello drautuna! We believe that this post does not fit the main topic of this site. Problem solved For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be ...
written 4.1 years ago by drautuna60
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Comment: C: Annovar: how to update sequence length based on deletion size
... Just what i needed, thanks. ...
written 4.1 years ago by drautuna60
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(Closed) Annovar: how to update sequence length based on deletion size
... Hi, so I'm using Annovar for its gene annotation capabilities and I need some help changing how the input is setup.   The complete command I run on Annovar for its gene annotation capabilities is:      ./annotate_variation.pl -geneanno -buildver hg19 MyData.avinput humandb Here is a small exampl ...
parsing annovar sequence bioinformatics written 4.1 years ago by drautuna60 • updated 4.1 years ago by Sam2.3k
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FANTOM5 TSS downloads by cell line
... Hi, I have a simple question to those of you familiar with using the fantom5 database on enhancers, promoters, and TSS's. I am currently in a project where I annotate variants, one of which is based on whether they fall into regions of importance, such as enhancers and TSS. I'm supposed to use the ...
fantom5 data cell lines written 4.4 years ago by drautuna60
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Comment: C: Downloading ENCODE regulation data in .bed format by cell line
... Actually, I have a quick followup question: How can one download all of the chip-seq data quickly? It is extraordinarily tedious to download each of the hundred histone modificiation and TFBS files one by one ...
written 4.5 years ago by drautuna60
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Comment: C: Downloading ENCODE regulation data in .bed format by cell line
... Thank you for the nearly instantaneous reply! Saved me a lot of time looking where to download the databases ...
written 4.5 years ago by drautuna60
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Downloading ENCODE regulation data in .bed format by cell line
... So, I have a list of variants I want to annotate based off several databases in .bed format. The rest of the databases I want to include are off of ENCODE, but despite my searches I cannot for the love of my life download the data off ENCODE based off cell line. I always end up at this page: http: ...
bed encode annotations databases cell line written 4.5 years ago by drautuna60 • updated 4.5 years ago by onuralp180
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Variant annotation using several .BED files
... So, I have a data file containing several hundred variants in the following format: CHR #       START POS      END POS     VARIANT ID     1              100                   1000             rs1 1              1200                  1400            rs2           I ran the latter through Annovar ...
bedtools annovar intersect annotation written 4.5 years ago by drautuna60 • updated 4.5 years ago by Aaronquinlan10k
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categorizing LD bodies and variants by SNP, cell layer, and DNA location
... Previously, I had a list of variants as well as whole genome data from several individuals in .TPED and .TFAM format. I (with the guidance of biostars users!) used plink to find out which variants are in LD with the list of variants.  Now that I have a combined list - that is, the original list of ...
linkage cell line disequilibrium plink variants written 4.5 years ago by drautuna60
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Comment: C: Filtering ASE variants with those in high LD using plink
... Thanks, it worked! I have another question now; the output of the latter gives me the file plink.tags, which consists of all the names of the original ASE SNPs as well as the SNPs in LD with those original SNPs.  In the .TPED, it has the data for all the SNPs - I want to extract, from this file, d ...
written 4.6 years ago by drautuna60

Latest awards to drautuna

Popular Question 3.9 years ago, created a question with more than 1,000 views. For Variant annotation using several .BED files
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Downloading ENCODE regulation data in .bed format by cell line
Popular Question 3.9 years ago, created a question with more than 1,000 views. For FANTOM5 TSS downloads by cell line

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