User: DataFanatic

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DataFanatic260
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Posts by DataFanatic

<prev • 156 results • page 1 of 16 • next >
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Comment: C: help clarify ways to measure coverage in RNA-Seq libraries
... Thank you for clarifying! ...
written 7 weeks ago by DataFanatic260
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help clarify ways to measure coverage in RNA-Seq libraries
... Can someone help clarify ways to measure coverage? Here is my current understanding, but I'm not sure about 2. 1. Library size is one way to measure coverage, and it is equal to 2. The number of reads that align to a particular gene. I hope this makes sense. Thanks! ...
coverage rna-seq written 7 weeks ago by DataFanatic260
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Comment: C: Understanding the colData in DESeq2
... Thank you, rpolicastro. I also found the answer to this on pg 14 of Beginner's guide to using the DESeq2 package. http://www.bioconductor.org/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf Do the following "to make sure that Control is the rst level in the treatment factor, so that the ...
written 8 weeks ago by DataFanatic260
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Comment: C: Understanding the colData in DESeq2
... Yes, this works thank you so much for your help! How would you " ignore this too and set the contrast manually when returning the results?" ...
written 8 weeks ago by DataFanatic260
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Comment: C: Understanding the colData in DESeq2
... Actually this will yield the same results: expdesign = read.delim("expdesign.txt") Also, DESeqDataSetFromMatrix will convert to factor with a warning which is why I am reading them as factors. ...
written 8 weeks ago by DataFanatic260
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Understanding the colData in DESeq2
... Hi, I am using DESEq2 to compute differential gene expression, and if I am interpreting this correctly, changing the names of categories in the colData reverses the test that is performed. The matrix counts is intact with 6 col and (WT)3 (hux)3. Here WT=wild type or control and hux=treatment. I w ...
coldata deseq2 lfc written 8 weeks ago by DataFanatic260
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Comment: C: HISAT2: does the parameter -k 1 means unique mapping?
... Is it incorrect to include all reads even those that map >1 times? I have always kept uniquely mapped. Also is there an option to keep only uniquely mapped using HISAT2? ...
written 8 weeks ago by DataFanatic260
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Comment: C: over-representation of sequences that map to "Drosophila melanogaster signal rec
... The data is intact, I just ran FastQC on the fastqc files. I said I was unsure not that I want to remove the sequences. I was hoping someone could explain if this is a typical artifact of Ribo-Seq data (others have posted a similar question with no answers yet). Thanks for your comment though. ...
written 8 weeks ago by DataFanatic260
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over-representation of sequences that map to "Drosophila melanogaster signal recognition particle
... I found over-representation(count:114784, 1.65%, No Hit) of sequences that map to "Drosophila melanogaster signal recognition particle" but with my current knowledge, I am still unsure whether I should remove these reads from my TRAP-Seq data. "signal recognition particle (SRP) controls the transp ...
srp representation trap-seq rna-seq fastqc written 8 weeks ago by DataFanatic260
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Comment: C: Discounting secreted proteins from with data of signal recognition particle tran
... I found enrichment of sequences that map to "Drosophila melanogaster signal recognition particle" but with my current knowledge I am still unsure what the function of these SRP is and whether I should remove these reads from my Ribo-Seq data. https://blast.ncbi.nlm.nih.gov/Blast.cgi#alnHdr_183419903 ...
written 8 weeks ago by DataFanatic260

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Popular Question 23 days ago, created a question with more than 1,000 views. For PCA from genotype data using the --pca option in plink2
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