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head gene_counts.gff sed -e 's/^.*locus_tag=//' < gene_counts.gff > gene_counts.tab |
After it has run, take a peek at the new file:
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head gene_counts.tab
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Now, we are going to load the GFF file straight into R, remove the columns we don't want, name the columns and rows like R expects, and write out this file. You could do this in any other scripting language, or even Excel. We will write out the first few lines of the file at each step, so that you can see what the command is doing.
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- What are the numbers returned by
sizeFactors( cds )?Expand Answer... Answer... They are, roughly speaking, the relative average coverage of each data set? There are roughly 5 times as many counts of reads in genes for wt2 as there are for mut2. Specifically, they are the size parameter of the negative binomial fit to the counts per gene per data file.
- What are the dispersion estimates?
Expand Answer... Answer... The model assumes there is also a per-gene aspect to the variance in counts observed, that is again fit to a negative binomial distribution (=overdispersed Poisson distribution). The program fits a model where In this model, the lower the counts are, the more dispersion relative to the mean is expected (red line in graph), and thus the less significant a change in counts becomes. Thus, higher fold changes are required in lowly expressed genes to call the same observed fold-change difference as significant.
- What was the predominant effect of the mutation on gene expression in this Listeria strain?
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