Include ALFA results for uniquely mapping reads
Currently, ALFA produces results for multi-mapping reads from STAR RPM's output UniqueMultiple.str1.out.bg and UniqueMultiple.str2.out.bg. That is, STAR computes RPM normalised coverage for uniquely and multi-mapping reads and stores it in the UniqueMultiple files.
ALFA uses these files and produces the ALFA_Categories.pdf and ALFA_Biotypes.pdf plots.
These give the nucleotide distributions for various features.
However, the distribution of uniquely mapping reads to the various features is currently not available.
One easy way to generate this distribution is to use the STAR RPM output files Unique.str1.out.bg and Unique.str2.out.bg and compute the ALFA plots from these files.