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- # Human globin protocol stats
- This is a pair of spreadsheets summarizing the globin-reducing
- properties of an experimental RNA-seq protocol.
- - [`method-select.xlsx`](method-select.xlsx) shows the results for
- several different methods of globin reduction. The most important
- column is "Non-HB", which represents the fraction of total reads
- that map to non-globin genes.
- - [`concentration-select.xlsx`](concentration-select.xlsx) shows the
- results of selecting the best globin blocking method and optimizing
- the concentration of blockers as well as the number of
- hybridizations.
- # Cyno globin plots
- This is a series of example plots for evaluation of a similar globin
- reduction protocol that was designed for cynomolgus monkeys.
- - [`BCVplots.pdf`](BCVplots.pdf) and [`corrplot.pdf`](corrplot.pdf)
- show, respectively, that the biological coefficient of variation is
- not increased, and the sample-to-sample correlation is not
- decreased, by the globin reduction protocol.
- - [`cyno-vs-hg19.pdf`](cyno-vs-hg19.pdf) shows excellent correlation
- between total read counts on the cyno and human genomes, indicating
- that the cyno annotation is reasonably complete.
- - [`pval-comparisons.pdf`](pval-comparisons.pdf) shows the comparison
- between p-values from edgeR, limma-voom, and DESeq2 on the exact
- same differential expression test. Surprisingly, despite the
- significant algorithmic differences, edgeR and limma are in quite
- close agreement. DESeq2 id overly liberal because it does not
- account for the negative estimation bias in negative-binomial
- dispersions.
- # Publication plots
- These are the figures from an upcoming publication on the developed
- globin blocking method.
- - [Figure 1](figure1 - globin-fractions.pdf): Globin blocking (GB)
- substantially increases yield and consistency of non-globin reads.
- - [Figure 2](figure2 - aveLogCPM-colored.pdf): GB lowers the noise
- floor and increases the distance between noise floor and signal.
- - [Figrue 3](figure3 - detection.pdf): GB allows detection of more
- genes at any abundance threshold.
- - [Figure 4](figure4 - maplot-colored.pdf): GB has small but
- systematic effects on other genes' measured expression levels.
- - [Figure 5](figure5 - corrplot.pdf): GB Significantly increases
- correlation between libraries.
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