User: spiral01

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spiral01100
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Posts by spiral01

<prev • 96 results • page 1 of 10 • next >
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Answer: A: Problems when installing Grapes and Bio++ tools
... Solved by downloading bpp-core, bpp-seq and bpp-phyl using sudo package manager. ...
written 7 months ago by spiral01100
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Problems when installing Grapes and Bio++ tools
... Hi, I am trying to install Grapes (available [here](https://github.com/BioPP/grapes)). I have already installed Bio++ using the instructions given [here](http://biopp.univ-montp2.fr/wiki/index.php/Installation). The Bio++ installation goes off fine, but when I try to install Grapes using the followi ...
software error written 7 months ago by spiral01100
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Comment: C: Bioawk - using bash variables
... Perfect. This works. Sorry but could explain why this change works? Thanks. ...
written 8 months ago by spiral01100
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Bioawk - using bash variables
... Hi, I am using bioawk to extract entries in a fasta file based on partial matches on IDs. Now normally I can use a bash variable in awk by assigning it using `-v`. However, when using bioawk, the variable does not seem to be stored as gene, and as such I get no matches. I have tested this using the ...
software error awk written 8 months ago by spiral01100 • updated 8 months ago by SMK1.9k
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.axt formats for pairwise alignments and how to convert to paml
... I am currently trying to calculate rates of substitution in humans, using the human-chimpanzee pairwise alignment found here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsPanTro6/ My problem is that the alignment is in the .axt format (explained here: https://genome.ucsc.edu/goldenPath/help/axt ...
alignment written 8 months ago by spiral01100 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: 1000 genomes coding SNPs not in exonic regions?
... Gah such a rookie error. Thank you! ...
written 13 months ago by spiral01100
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Comment: C: 1000 genomes coding SNPs not in exonic regions?
... I need to obtain the exon that each SNP lies in, as well as the start and end co-ordinates (because my ultimate goal is to identify the length of the specific exon that each SNP lies in). The available GENCODE annotation of 1000 genomes variants provides the exon number within the gene, but not the ...
written 13 months ago by spiral01100
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Comment: C: 1000 genomes coding SNPs not in exonic regions?
... The 1000 genomes data is available with consequence annotations here: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/functional_annotation/. I then simply parse the variants for those that have a missense or synonymous consequence annotation. ...
written 13 months ago by spiral01100
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Comment: C: 1000 genomes coding SNPs not in exonic regions?
... I am getting the data with GENCODE annotations here: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/functional_annotation/ ...
written 13 months ago by spiral01100
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Comment: C: 1000 genomes coding SNPs not in exonic regions?
... Hi, thanks for the response. Yes I can confirm that the ref genomes are the same, hg38. ...
written 13 months ago by spiral01100

Latest awards to spiral01

Scholar 7 months ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Popular Question 13 months ago, created a question with more than 1,000 views. For Phylogenetics in R: obtaining internal branch lengths
Popular Question 13 months ago, created a question with more than 1,000 views. For How large are 1000genomes vcf files?
Popular Question 13 months ago, created a question with more than 1,000 views. For Calculating LRT of a phylogenetic tree (as in codeml)
Popular Question 13 months ago, created a question with more than 1,000 views. For Acquiring and combining hg38 SNP and gene data
Popular Question 13 months ago, created a question with more than 1,000 views. For vcf files: counting number of variants in genomic windows of chosen size
Popular Question 13 months ago, created a question with more than 1,000 views. For Calculating Tajima's D from vcf data using bed files
Popular Question 13 months ago, created a question with more than 1,000 views. For Quickest way to filter vcf using bed files
Popular Question 13 months ago, created a question with more than 1,000 views. For Writing vcf file headers
Popular Question 22 months ago, created a question with more than 1,000 views. For Phylogenetics in R: obtaining internal branch lengths
Great Question 22 months ago, created a question with more than 5,000 views. For Rooting phylogenetic trees in R using Ape's root function: Trees don't seem to root.
Scholar 23 months ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Supporter 2.2 years ago, voted at least 25 times.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Rooting phylogenetic trees in R using Ape's root function: Trees don't seem to root.

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