Transcript assembly and quantification for RNA-Seq
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README.md

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 make release.

Running StringTie

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