A method for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes
Download to some executable path and type SLaPMapper.pl
Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
fastqjoin https://expressionanalysis.github.io/ea-utils/
trimmomatic http://www.usadellab.org/cms/?page=trimmomatic
please modify paths to executables in the subroutine called "paths" at the top of the script.
Fiebig, M., Gluenz, E., Carrington, M., and Kelly, S. (2014). SLaP mapper: A webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes. Molecular and Biochemical Parasitology 196(2):71-4