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cookie20
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Posts by cookie

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Trimming with ShortRead
... Hi, I am using the ShortRead package to analyze my fastq files. Could someone explain to me how does the function trimtails in this package function? My plan is find certain positions with a lower quality score and to trim these positions from my fastq file. How can one do this? I am rather confu ...
shortread written 2.6 years ago by cookie20 • updated 2.6 years ago by Martin Morgan ♦♦ 20k
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Calculate the expression of gene
... Hi, I am trying to figure out how to calculate the expression of a gene via GenomicFeatures and IRanges. My solution to this is based on the idea where I find group the TxDb by genes, then see if how many transcripts are "above" the gene, that is how many are overlapping, within the range of the g ...
iranges genomicranges written 2.7 years ago by cookie20 • updated 2.7 years ago by James W. MacDonald45k
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Comment: C: Intergenic coordinates with Genomic Feaures
... Thank you again for answering again. Well, I can see what you are trying to tell me. But, I many more questions: 1) When I group by a gene, does that mean in the output I have just the genes and nothing else? If yes, then this does not make any sense to me. First, this is a TxDb object, so it has ...
written 2.7 years ago by cookie20
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Plot coverage in a presentation for GenomicFeatures
... Hi,  I found a presentation about the GenomicFeatures and its basic function. In there, I found a function called plotCoverage. I am interested in what it does. Can someone explain it to me? plotCoverage <-function(x, chrom, start=1, end=length(x[[chrom]]), col="blue", xlab="Index", ylab ...
genomicfeatures written 2.7 years ago by cookie20 • updated 2.7 years ago by Michael Lawrence9.8k
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Comment: C: Intergenic coordinates with Genomic Feaures
... And do I have to take notice about the "+" or "-" strand? ...
written 2.7 years ago by cookie20
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Comment: C: Intergenic coordinates with Genomic Feaures
... Thanks you for your comment! Can you please also comment my way? Is that the right logic applied to the problem? ...
written 2.7 years ago by cookie20
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Intergenic coordinates with Genomic Feaures
... Hi, I would like to extract the coordinates for a chromosome. I made a chunk of code, but as I am new to these packages, I am not sure if I follow the right logic here:   library(IRanges) library(GenomicFeatures) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb = transcriptsBy(TxDb.Hsapiens.UCSC.h ...
iranges genomicfeatures genomicranges written 2.7 years ago by cookie20 • updated 2.7 years ago by Mike Smith2.1k
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Comment: C: Introns at transcript expression level
... This is quite interesting. Is there a paper on this? I am interested how it is possible exon +1 is equal introns. ...
written 2.7 years ago by cookie20
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Comment: C: Introns at transcript expression level
... Thanks a lot! ...
written 2.7 years ago by cookie20
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Introns at transcript expression level
... Hi, I am trying to get the average number of introns per transcripts in the human genome. I am new to this, but I concluded that I have to use the package GenomicFeatures or Iranges. Thus far I have made this code chuck: library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb = TxDb.Hsapiens.UCSC.hg19.kn ...
iranges genomicfeatures written 2.7 years ago by cookie20 • updated 2.7 years ago by Hervé Pagès ♦♦ 13k

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