Obtaining and installing StringTie

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The current version of StringTie can be downloaded from

http://ccb.jhu.edu/software/stringtie

In order to build StringTie from the source package,

the following steps should be taken:

* Unpack the downloaded StringTie source archive in a directory of your choice, e.g.:

cd ~/src/

tar xvfz ~/Downloads/stringtie-V.V.V.tar.gz

A directory called stringtie-V.V.V (where V.V.V is the current

numeric version of the program) will be created in the current directory.

* Change to that directory and build the stringtie executable:

cd stringtie-V.V.V

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 the

`make release` command.

Running StringTie

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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 alignments

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