User: gtho123

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gtho123210
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Posts by gtho123

<prev • 32 results • page 1 of 4 • next >
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SolexaQA++ lengthsort - c output
... I am looking for advice on the output of `SolexaQA++ lengthsort - c` when preprocessing my RNA-Seq data. Having already used `SolexaQA++ dynamictrim` to trim by read quality I then sought to remove any short reads which resulted using `SolexaQA++ lengthsort` and as the data is paired end I used the ...
next-gen sequencing written 18 months ago by gtho123210 • updated 18 months ago by Brian Bushnell16k
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Use Bedtools to extract stranded read depth from BAM files
... I am trying to use Bedtools to read-depth counts to generate plots of RNA-Seq read coverage like one sees in genome browsers. I am running into difficulty doing this in a strand specific manner. I know my data is strand-specific and I am informed that the alignment was done using Tophat2 specifying ...
bedtools alignment rna-seq written 2.6 years ago by gtho123210 • updated 2.6 years ago by michael.ante3.2k
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Forge a BSgenome data package
... My supervisor has requested that I create coverage plots to visualize BAM alignments of RNA-Seq data. I though a good way to do this would be to use Gviz. We work on the model legume Medicago truncatula which does not have a BSgenome package so I though I'd try and make one. Following the vignette ...
bioconductor bsgenome gviz biostrings written 3.5 years ago by gtho123210 • updated 3.5 years ago by karl.stamm3.4k
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Sequence clustering and motif identification.
... I have a alignment of >300 homologous sequences from different samples. All are the same length at around 15,000 bases. I don't expect any to be identical but wish to cluster them and identify the (motifs or individual bases) which distinguish or are more characteristic of each cluster than from ...
alignment sequence clustering motifs written 3.9 years ago by gtho123210 • updated 3.9 years ago by dago2.5k
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Answer: A: R programming: match and rearrange
... I don' think I quite understand what you are trying to do but from your example it seems like you want to insert the appropriate `GeneX.AD` value from the `Genotype` vector to immediately after the corresponding `GeneX.GT` element in the `Names` vector. If this is the case you could use regular exp ...
written 3.9 years ago by gtho123210 • updated 6 months ago by RamRS20k
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Answer: A: Generate genotype specific FASTA sequences from VCF file and reference sequence
... It turns out that when creating individual VCF files using the SelectVariants tool there is a optional flag -env which needs to be called too. The docs say that it is called to not "include loci found to be non-variant after the subsetting procedure". I find the interpretation of this confusing but ...
written 3.9 years ago by gtho123210
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Generate genotype specific FASTA sequences from VCF file and reference sequence
... I have some VCF files, each of which I have merged to contain >300 genotypes. Furthermore, to make them more manageable I have subsetted them to just contain the chromosome regions I am interested in. Now I wish to generate some genotype specific FASTA sequences using these files and a reference ...
gatk sequence snp written 3.9 years ago by gtho123210 • updated 3.9 years ago by Len Trigg1.2k
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Answer: A: Visualize a genome
... It sounds like you want to construct a karyogram. You can do this with an R package called ggbio. See section 4.3 in the vignette or this demo in the docs. Basically you plot the chromosomes and fill them in based on the quantitative value you assign to it.   ...
written 3.9 years ago by gtho123210
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Answer: A: Help with graphing ANOVA results in R
... I am unsure where the error occurred however if I understand you correctly you want to perform an ANOVA on your "functional_nonfunctional" column using the different habitats as factors. While I am unable to use the "aov.phylo" function as I don't have the phylogenetic information I think I can help ...
written 4.1 years ago by gtho123210
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Comment: C: Help with graphing ANOVA results in R
... It would help if you added a little of what your data looked like, even just the first few lines of your data.frame. Use: head(data) Also there are some inconsistencies in your code such as row 5 is not given a group (eg. is it volant, terrestrial or other?) also you reassign the name Group and x ...
written 4.1 years ago by gtho123210

Latest awards to gtho123

Popular Question 18 months ago, created a question with more than 1,000 views. For Use Bedtools to extract stranded read depth from BAM files
Popular Question 18 months ago, created a question with more than 1,000 views. For Forge a BSgenome data package
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Generate genotype specific FASTA sequences from VCF file and reference sequence
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Identify Duplicates In Two Fasta Files But Not Merge Them
Popular Question 3.5 years ago, created a question with more than 1,000 views. For gffread is not working
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Bioconductor - Error : Function found is not S4 generic
Student 3.5 years ago, asked a question with at least 3 up-votes. For gffread is not working
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Genomic Features - makeTranscriptDbFromGFF()
Popular Question 3.9 years ago, created a question with more than 1,000 views. For gffread is not working
Scholar 3.9 years ago, created an answer that has been accepted. For A: Bioconductor - Error : Function found is not S4 generic
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Bioconductor - Error : Function found is not S4 generic
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Bioconductor - Error : Function found is not S4 generic
Scholar 4.5 years ago, created an answer that has been accepted. For A: Bioconductor - Error : Function found is not S4 generic

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