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‎README‎

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‎README.md‎

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## Obtaining and installing StringTie
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In order to build StringTie from this GitHub repository
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the following steps can be taken:
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Source and binary packages for this software, along with a small test data set
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can be directly downloaded from the <a href="https://github.com/mpertea/stringtie2/releases">Releases</a> page for this repository. StringTie is compatible with a wide range of Linux and Apple OS systems (going as far back as RedHat Enterprise Linux 5.0 and OS X 10.7). The main program (StringTie) does not have any other library dependencies and in order to compile it from source it requires only a C++ compiler which supports the C++ 0x standard (GCC 4.5 or newer).
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### Building the latest version from the repository
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In order to compile the StringTie source in this GitHub repository the following steps can be taken:
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```
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git clone https://github.com/mpertea/stringtie2
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cd stringtie2
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make release
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```
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Note that simply running `make` will produce an executable
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which is more suitable for debugging and runtime checking but which can be
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significantly slower than the optimized version which is obtained by using
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`make release`.
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If the compilation is successful, the resulting `stringtie` binary can then be copied to
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a programs directory of choice.
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Installation of StringTie this way should take less than a minute on a regular Linux or Apple MacOS
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desktop.
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### Installation of the super-reads module (optional)
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Note that simply running `make` would produce an executable which is more suitable for debugging
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and runtime checking but which can be significantly slower than the optimized version which
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is obtained by using `make release` as instructed above.
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This optional module can be used to de-novo assemble, align and pre-process
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RNA-Seq reads, preparing them to be used as "super-reads" by Stringtie.
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### Using pre-compiled (binary) releases
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Instead of compiling from source, some users may prefer to download an already compiled binary for Linux
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and Apple OS X, ready to run. These binary package releases are compiled on older versions of these
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operating systems (RedHat Enterprise Linux 5.0 and OS X 10.7) in order to provide compatibility with
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a wide range of (older) OS versions, not just the most recent versions. These precompiled packages are
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made available on the <a href="https://github.com/mpertea/stringtie2/releases">Releases</a> page for this repository.
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Please note that these binary packages do not include the optional [super-reads module](#the-super-reads-module),
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which currently can only be built on Linux machines, from the source made available in this repository.
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Mode detailed information is provided in the SuperReads_RNA/README.md
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Quick installation instructions for this module (assuming the above Stringtie installation
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was completed):
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```
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cd SuperReads_RNA
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./install.sh
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```
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#### Using super-reads with Stringtie
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After running the super-reads module (see the SuperRead_RNA/README.md file for usage details), there
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is a BAM file which contains sorted alignment for both short reads and super-reads, called *`sr_merge.bam`*,
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created in the selected output directory. This file can be directly given as the main input file
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to StringTie as described in the _Running Stringtie_ section below.
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## Running StringTie
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sorted by genomic location (for example the accepted_hits.bam file produced
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by TopHat).
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The main output of the program is a GTF file containing the structural definitions of the transcripts assembled by StringTie from the read alignment data. The name of the output file should be specified by with the `-o` option.
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### Running StringTie on the provided test/demo data
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When building from this source repository, after the program was compiled with `make release` as instructed above, the generated binary can be tested on a small data set with a command like this:
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```
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make test
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```
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This will run the included `run_tests.sh` script which downloads a small test data set
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and runs a few simple tests to ensure that the program works and generates the expected output.
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If a pre-compiled package is used instead of compiling the program from source, the `run_tests.sh` script is included in the binary package as well and it can be run immediately after unpacking the binary package:
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```
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tar -xvzf stringtie-2.0.Linux_x86_64.tar.gz
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cd stringtie-2.0.Linux_x86_64
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./run_tests.sh
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```
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These small test/demo data sets can also be downloaded separately as <a href="https://github.com/mpertea/stringtie2/releases/download/v2.0/test_data.tar.gz">test_data.tar.gz</a> along with the source package and pre-compiled packages on the <a href="https://github.com/mpertea/stringtie2/releases">Releases</a> page for this repository.
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The tests can also be run manually as shown below (after changing to the _test_data_ directory, `cd test_data`):
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#### Run 1: Input consists of only alignments of short reads
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```
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stringtie -o short_reads.out.gtf short_reads.bam
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```
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#### Run 2: Input consists of alignments of short reads and superreads
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```
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stringtie -o short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
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```
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#### Run 3: Input consists of alignments of long reads
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```
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stringtie -L -o long_reads.out.gtf long_reads.bam
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```
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#### Run 4: Input consists of alignments of long reads and reference annotation (guides)
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```
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stringtie -L -G human-chr19_P.gff -o long_reads_guided.out.gtf long_reads.bam
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```
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The above runs should take around one second each on a regular Linux or MacOS desktop.
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(see also <a href="https://github.com/mpertea/stringtie2/blob/master/test_data/README.md">test_data/README.md</a>).
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For very large data sets one can expect up to one hour of processing time. A minimum of 8GB of RAM is recommended for running StringTie on regular size RNA-Seq samples, with 16 GB or more being strongly advised for larger data sets.
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### StringTie options
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The following optional parameters can be specified (use -h/--help to get the
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usage message):
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```
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the input alignment data by StringTie and not present in the reference file will be
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printed as well ("novel" transcripts).
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## The super-reads module
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This optional module can be used to de-novo assemble, align and pre-process
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RNA-Seq reads, preparing them to be used as "super-reads" by Stringtie.
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Mode detailed information is provided in the
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<a href="https://github.com/mpertea/stringtie2/blob/master/SuperReads_RNA/README.md">SuperReads_RNA/README.md</a>.
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Quick installation instructions for this module from the source available on this repository
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(assuming the above Stringtie installation was completed):
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```
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cd SuperReads_RNA
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./install.sh
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```
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### Using super-reads with Stringtie
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After running the super-reads module (see the <a href="https://github.com/mpertea/stringtie2/blob/master/SuperReads_RNA/README.md">SuperReads_RNA</a> module documentation for usage details), there
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is a BAM file which contains sorted alignment for both short reads and super-reads, called *`sr_merge.bam`*,
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created in the selected output directory. This file can be directly given as the main input file
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to StringTie as described in the [Running StringTie](#running-stringtie) section above.
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## License
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StringTie is free, open source software released under an <a href="https://opensource.org/licenses/MIT">MIT License</a>.

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