HOMER can produce tag counts of selected regions (tss or from peak files).
ReadCounts will read this data in tidy up the column names and cast
the matrix as numeric, and finally return a data.table object for use with
Location of raw tag counts data from HOMER.
data.table of counts data with annotation and tidy columns.
This counts table can be produced using the
from the NewSeq pipeline, which runs the following command over multiple
annotatePeaks.pl tss mm10 -ann $GTF -size $SIZE -log -d $TAGDIRS