User: Karl

gravatar for Karl
Karl330
Reputation:
330
Status:
New User
Location:
USA
Last seen:
7 years, 2 months ago
Joined:
8 years ago
Email:
u2074

Posts by Karl

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Calculating Z-Scores
... z-score implies normal distribution. Check out "deseq" for this task instead. ...
written 7.5 years ago by Karl330
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Comment: C: Microarray Data Without Replicates. Any Hope To Get Something Out Of It?
... DESeq only works for count-data, as in reads per region, and will not apply to array intensity data. ...
written 7.6 years ago by Karl330
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Comment: C: Distance Between The Genes.
... Beware overlapping genes. You might even find a small gene tucked inside of a large gene's intron. ...
written 7.6 years ago by Karl330
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Answer: A: Get Coding Snps For 1000 Genomes Data
... To find polymorphisms in a gene of interest, I would get the gene's general region as chromosome and start/stop location (plus a kilobase or ten on each end for regulatory regions). Then go to Ensembl or Biomart or dbSNP and ask for known variants in that region. ...
written 7.8 years ago by Karl330
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Answer: A: Enrichment Methods In Metagenomics
... It would help if you could explain your specific scenario in more detail. What exactly are you trying to do? I've worked with pathway analysis (a little), and I gather the important tests are about random graphs. Given some gene co-expression graph, and the set of known genes, we could construct ra ...
written 7.8 years ago by Karl330
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Comment: C: Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?
... This isn't a forum, it's Q&A. If you have a new question, make a new post so people will see it. ...
written 7.8 years ago by Karl330
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Answer: A: Meaning Of Fpkm Value Used By Cufflinks
... Tophat has aligned your reads to the reference genome, and marked those reads which align with and without splice junctions. It's intended for transcriptome analysis, or RNA-Seq. That way, anything that maps unspliced must be an exon and anything that jumps regions must span an intron. Cufflinks ...
written 7.8 years ago by Karl330
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Answer: A: Help Needed About Snp And Genomic Co-Ordinates.
... A SNP is just a single nucleotide change. A gene could carry a thousand of them, and the regions nearby a gene could carry a thousand more that also play a role. Usually we define SNP with some threshold of population abundance. If your whole population shares the same allele at a site, that SNP is ...
written 7.9 years ago by Karl330
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Comment: C: Extract User Defined Region From An Fasta File
... This is not a discussion forum, It's Q&A. Youve posted this as an 'answer' which doesn't make sense. To reply to another answer use the comment button underneath it, like I am here. ...
written 7.9 years ago by Karl330
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Comment: C: Alignment Free Cog Detection Program
... What's a COG category? Can you elaborate on the problem? ...
written 7.9 years ago by Karl330

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