Compare two libraries

Post date: May 18, 2016 4:40:10 PM

The best way to compare two libraries (e.g. wt vs mutant or condition 1 vs condition 2) is to plot the number of transposon in each gene in the two libraries:

plot(library1.tnpergene,library2.tnpergene,'.')

Outliers can be identified using gname and clicking on them:

gname(names)

Note that the variable names should be loaded

A similar analysis can be performed by plotting the number of sequencing read per gene, instead:

plot(library1.readpergene,library2.readpergene,'.')