#### INFO SSRC - counts mapped reads for given annotation file counts splitted reads only once counts strand specific counts on exons or whole genes calculates TPM values #### INSTALLATION All libraries and tools will be installed locally without root permissions To remove SSRC completely, just delete the installation directory # Download latest SSRC wget https://github.com/rna-hta-jena/ssrc/archive/master.zip # Extract library unzip master.zip # Enter extracted directory cd ssrc-master # Set programs installation path export PROGRAMS=$HOME/programs/ # install samtools bash install_samtools.sh # export samtools installation for Perl Module installation export SAMTOOLS=$PROGRAMS/samtools-0.1.19 # Set module installation path export MODINSTALL=$HOME/perl5 # Tell Perl where to find modules export PERL5LIB=$MODINSTALL/lib/perl5:$PERL5LIB # Make this permanent echo 'export PERL5LIB='$PERL5LIB >> $HOME/.bashrc # Start installation ./cpanm -l $MODINSTALL . # copy scripts to programs directory cp *.pl $PROGRAMS #### RUN perl Split_senstive_read_counter.pl -h #### CONTACT Konstantin Riege Chair of Bioinformatics High Throughput Analysis Friedrich-Schiller-University Jena http://www.rna.uni-jena.de konstantin{.}riege{a}uni-jena{.}de