Obtaining and installing StringTie
The current version of StringTie can also be downloaded from http://ccb.jhu.edu/software/stringtie
In order to build StringTie from this GitHub repository the following steps can be taken:
git clone https://github.com/gpertea/stringtie cd stringtie make release
Note that simply running
make will produce an executable
which is more suitable for debugging and runtime checking but which can be
significantly slower than the optimized version which is obtained by using
Run stringtie from the command line like this: ''' stringtie [options] <aligned_reads.bam> ''' The main input of the program is a SAMTools BAM file with RNA-Seq mappings sorted by genomic location (for example the accepted_hits.bam file produced by TopHat).
A list of parameters and options for the program can be obtained by running the program with only the -h or --help option.
More detailed usage instructions can be found on the StringTie website: http://ccb.jhu.edu/software/stringtie