User: nancy

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nancy60
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Posts by nancy

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RNA-seq data analysis for differential expression of a single gene
... I have some RNA-seq data for a large number of samples (treated vs control), to the order of ~50M PE reads per sample, from mouse. These data have not been aligned yet to the reference genome. I am, however interested in the expression level of one single target gene across all these samples, and a ...
rna-seq written 10 days ago by nancy60 • updated 10 days ago by JC7.0k
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Are there minimum requirements from a de novo genome assembly for it to be suitably used as a reference for SNP calling?
... To what extent does a de novo genome need to be assembled for it to be used as a reference? If I have a de novo assembly for a large mammalian genome comprising of a under 1M contigs (Illumina + PacBio), and I want to call SNPs against this reference from samples that have been sequenced (shallow 5 ...
assembly reference genome snp wgs written 4 months ago by nancy60
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RNA-seq data analysis to detect dosage effect or proportional increase/decrease in expression across a series
... Hi- I have some RNA-seq data from a series of 4 isogenic strains (0,1,2,3), differing in their copy number of a single gene. I would now like to identify those genes whose expression changes across these samples in proportion to the copy number of the gene of interest. For e.g., in the series 0,1, ...
dosage effect deseq2 rna-seq written 5 months ago by nancy60 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: How to filter for samples that show good concordance across replicates in DESEQ2
... Thanks for your detailed and well-explained response, I actually understood it and it makes sense to me now. And thanks for cleaning up my original post too. I learned something there too! ...
written 6 months ago by nancy60
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Comment: C: How to filter for samples that show good concordance across replicates in DESEQ2
... Hi WouterDeCoster, Thanks for showing me how to add figures to the main post. Very useful! I quite disagree with as extreme a view as "any comparison with n=2 entirely invalid and all time you spend is wasted". Often, we do an exploratory n=2 to figure out things like most appropriate timepoint, ...
written 6 months ago by nancy60
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Comment: C: How to filter for samples that show good concordance across replicates in DESEQ2
... Thanks Kevin, 1. No, I do not believe every gene to go down in treated, sorry I grabbed two different sets of data (one from the UP sheet and one from the DOWN sheet) as representative examples of high variance vs good replicates. 2. I didn't generate Cooks Distance- have only 2 reps? but let me t ...
written 6 months ago by nancy60 • updated 6 months ago by zx87546.1k
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Comment: C: hclust heatmap clustering produce different relationships with fpkm versus rlog
... Hi Kevin, Thank you for your detailed reply. It will take me a while to assimilate and understand in as great detail. Having been on the lab side for several years, managing an NGS core lab - the only thing that strikes to me as odd is this part "NGS, samples are always sequenced to different depth ...
written 6 months ago by nancy60
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How to assess extent of cell-type admixtures from bulk RNA-seq data for a single tissue?
... We have bulk RNA-seq data from different samples (1 single tissue), treated vs control, (2 to 3 replicates each), and suspect that inherent cell-type heterogeneity is confounding our observations of D.E. We have no prior information on the levels of heterogeneity for these samples, however, looking ...
deconvolution scrna-seq cellmix rna-seq written 6 months ago by nancy60 • updated 6 months ago by YaGalbi1.4k
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Comment: C: hclust heatmap clustering produce different relationships with fpkm versus rlog
... Hi Kevin, "In saying that, it makes sense that correlation distance produces the same dendrogram between log2FPKM and the rlog counts because correlation, the statistical measure, is 'mostly' independent of the library size difference that I mentioned earlier (if you think about it, correlation jus ...
written 6 months ago by nancy60
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Comment: C: How to filter for samples that show good concordance across replicates in DESEQ2
... Thanks Andrew, I will check this function. However, it still strikes me odd that a p-value as low as p<10-5 is ascribed to a D.E. event where the two replicates show such little concordance. Since a low p-value indicates the event did not occur by chance, it is a bit counter-intuitive in these ca ...
written 6 months ago by nancy60

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Scholar 8 months ago, created an answer that has been accepted. For A: 6-bp deletions in RNA-seq data

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