User: spiral01

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spiral01100
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Posts by spiral01

<prev • 99 results • page 1 of 10 • next >
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Masking selected sites in human genome
... I am looking for a genome track that has masked selected sites (i.e. regions under natural selection) in the human genome, though I cannot find what I am looking for. Does anyone have any suggestions? Thanks. ...
genome assembly mask written 7 months ago by spiral01100
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Comment: C: Removing GC dinucleotides from a sequence
... Hi, please see the edit. Thanks. ...
written 10 months ago by spiral01100
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Removing GC dinucleotides from a sequence
... I have gene alignments between humans and chimpanzees and I need to remove GC dinucelotides between humans and chimpanzees. My question involves the best way to proceed with this. Is it at the codon level or at the sequence level? For instance, if I have the sequence `ACTGCA` this can be split int ...
gene alignment sequence snp written 10 months ago by spiral01100
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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 18 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 18 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 19 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 19 months ago by spiral01100 • updated 19 months ago by AK2.0k
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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 19 months ago by spiral01100 • updated 19 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 2.0 years 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 2.0 years ago by spiral01100

Latest awards to spiral01

Popular Question 9 months ago, created a question with more than 1,000 views. For Calculating LRT of a phylogenetic tree (as in codeml)
Popular Question 9 months ago, created a question with more than 1,000 views. For Calculating LRT of a phylogenetic tree (as in codeml)
Epic Question 16 months ago, created a question with more than 10,000 views. For Rooting phylogenetic trees in R using Ape's root function: Trees don't seem to root.
Popular Question 16 months ago, created a question with more than 1,000 views. For Parsing PhyloXML to split gene trees at duplication nodes
Popular Question 16 months ago, created a question with more than 1,000 views. For Calculating LRT of a phylogenetic tree (as in codeml)
Popular Question 16 months ago, created a question with more than 1,000 views. For Denisovan and Neanderthal vcf files
Popular Question 16 months ago, created a question with more than 1,000 views. For Annovar: Error when downloading dm6 drosophila database
Popular Question 16 months 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.
Popular Question 16 months ago, created a question with more than 1,000 views. For Set ancestral alleles to upper case in vcf file
Popular Question 16 months ago, created a question with more than 1,000 views. For Denisovan and Altai Neanderthal .bed files?
Popular Question 16 months ago, created a question with more than 1,000 views. For Using multiple filters in BiomaRt's getSequence
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Rooting phylogenetic trees in R using Ape's root function: Trees don't seem to r
Scholar 18 months ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Phylogenetics in R: obtaining internal branch lengths
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How large are 1000genomes vcf files?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Calculating LRT of a phylogenetic tree (as in codeml)
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Acquiring and combining hg38 SNP and gene data
Popular Question 2.0 years 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 2.0 years ago, created a question with more than 1,000 views. For Calculating Tajima's D from vcf data using bed files
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Quickest way to filter vcf using bed files
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Writing vcf file headers
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Phylogenetics in R: obtaining internal branch lengths
Great Question 2.8 years 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 2.8 years ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Supporter 3.1 years ago, voted at least 25 times.

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