User: Dave Tang

gravatar for Dave Tang
Dave Tang160
Reputation:
160
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Trusted
Location:
Australia
Website:
https://davetang.org/muse
Twitter:
davetang31
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Google Scholar Page
Last seen:
20 hours ago
Joined:
4 years, 9 months ago
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d***************@gmail.com

Genomics researcher.

Posts by Dave Tang

<prev • 29 results • page 1 of 3 • next >
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Comment: C: ploting a network of mRNAs and miRNAs
... I would recommend igraph as well and found this tutorial extremely useful: http://kateto.net/netscix2016 ...
written 10 months ago by Dave Tang160
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Comment: C: How to download VCF file of a specific human gene?
... I'm not quite sure what you have to do but I would imagine you don't need to download gene sequences. Perhaps this paper may be relevant https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5 for your thesis. ...
written 10 months ago by Dave Tang160
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Comment: C: How to download VCF file of a specific human gene?
... The Variant Caller Format (VCF) is used to store genetic variants that have been called/detected with respect to some reference. Here's a guide that I found useful http://www.internationalgenome.org/wiki/Analysis/vcf4.0. As for your question, they are two separate things. It is not difficult to con ...
written 10 months ago by Dave Tang160
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Comment: C: Allele frequency calculation
... I would expect that AFs will be more similar amongst related individuals. Depending on what you want to do, there are methods for adjusting for relatedness. ...
written 10 months ago by Dave Tang160
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Comment: C: Allele frequency calculation
... You could use GATK SelectVariants to subset the VCF file accordingly and then calculate the AF. ...
written 10 months ago by Dave Tang160
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Comment: C: Where can I get exome vcf file from the 1000 genome project?
... Hi Kelly, I came across this question because I wanted exome VCF files. In the end I couldn't find any and I downloaded the FASTQ data and called variants myself. I also subsetted the target exon regions from the WGS data. As you surmised, it is quite different from calling variants from exome data ...
written 11 months ago by Dave Tang160
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Answer: A: Summarise genotypes in a VCF file
... Use vcflib available at https://github.com/vcflib/vcflib and the vcffixup tool. cat output.vcf | grep -v "^#" | head -1 chr21 9889293 rs28676788 G A . . . GT 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/0 0/0 1/0 1/0 ...
written 11 months ago by Dave Tang160
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Comment: C: Delete rows in dataframe in R
... Fair enough. I thought filter() would easily address the problem but there's no straightforward way of filtering on all columns. ...
written 13 months ago by Dave Tang160
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Comment: A: Delete rows in dataframe in R
... I highly recommend the dplyr package by Hadley Wickham: https://cran.rstudio.com/web/packages/dplyr/vignettes/introduction.html. ...
written 13 months ago by Dave Tang160
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Comment: C: Agilent SureSelect XT Human All Exon +UTR v5
... Thanks for the reply Vijay. On my second try, I asked to join another workgroup and it was accepted (SureDesign: Join workgroup request accepted, account activated.) and I could download the required BED files. In my previous attempt about a year ago, I did try to email Agilent but they never got ba ...
written 13 months ago by Dave Tang160

Latest awards to Dave Tang

Popular Question 3 months ago, created a question with more than 1,000 views. For TruSeq Exome Enrichment Kit Targeted Regions BED File
Popular Question 11 months ago, created a question with more than 1,000 views. For H3K4Me3 ChIP-Seq signal at promoter
Popular Question 22 months ago, created a question with more than 1,000 views. For How To Create A "Discovery Plot"
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How To Create A "Discovery Plot"
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Free Linux server for bio-computing?

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