Moderator: swbarnes2

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Posts by swbarnes2

<prev • 307 results • page 1 of 31 • next >
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Answer: A: Why GWASs cannot speculate what kind of mutation the SNP would cause?
... It's easy to predict the amino acid change consequence of a mutation. What's hard is to predict the **functional** consequences of most changes. ...
written 9 days ago by swbarnes23.1k
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Comment: C: How do you extract data coordinates from PCA in R?
... "scale" in prcomp changes all the input values to give you an SD of 1 for each sample. That affects how the pca$x values come out, but not how they are plotted. ...
written 11 days ago by swbarnes23.1k
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Comment: C: trying to use DESeq2, how to set up the data files
... Check to make sure the sample names are exactly alike between the two files. I'd use nothing but letters, numbers, and underscores. ...
written 15 days ago by swbarnes23.1k
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Comment: C: trying to use DESeq2, how to set up the data files
... No one can evaluate that line of code by itself. (Though if I had to guess, I'd say that if you have 12 samples, your conditions vector needs 12 elements, not 2) You do not have to construct the conditions file in R; you can make it in excel and import it. I strongly recommend doing that, since y ...
written 16 days ago by swbarnes23.1k
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Comment: C: Designed primers with 3 bp mutations (codons) how to validate/visualize them?
... What command line options did you use? I would be surprised if it were impossible to relax the alignment stringency enough to allow something with 3 mismatches to align. But I wonder if bwa is making the alignment seed with your altered codon in the middle? Maybe making them again, with more than ...
written 17 days ago by swbarnes23.1k
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Answer: A: Sequences information from BAM file
... There are basically two reasons that your reads would be trimmed like that...for quality reasons, or because the read read all the way through to adapter. If it's adapter, you definitely want that trimmed away. If it's for quality reasons..you probably want it trimmed away. You'll have to ask who ...
written 17 days ago by swbarnes23.1k
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Answer: A: featureCounts generates low assigned rate
... The simple, but annoying, advice is to go back to where you got your genome and your gtf, and make sure they came from the sample place. If they didn't, get fresh ones from, say, ensembl, and redo the alignment. ...
written 17 days ago by swbarnes23.1k
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Answer: A: Computer logistics of comparing genomes within same individual
... First, stop and think. The last thing you want to do is re-invent the wheel. Plenty of people already do look at the differences between, say, normal and cancer cells. It's not like this is some brilliant idea that no one has ever heard of before. You need to understand what people already do, a ...
written 17 days ago by swbarnes23.1k
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Answer: A: How do I subset gene loci with no difference from DeSeq2 output?
... If the number in "log2FoldChange" is negative, that's down regulated. The NAs are usually genes with so few counts the software can't draw any conclusions about their expression. You'll have to ignore those. ...
written 18 days ago by swbarnes23.1k
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Answer: A: trying to use DESeq2, how to set up the data files
... It will be easier for you to do this in Excel. Make an excel sheet with your counts, every gene a row, every sample a column. Do put the gene names as the first column, and the sample names as the header row. That's the first file DESeq wants as input. The second is a file with the first column ...
written 18 days ago by swbarnes23.1k

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