A new and fast transcript assembler and abundance estimator for RNA-seq data.
Similar to Cufflinks, StringTie assembles transcripts from the alignments
produced by TopHat, including novel isoforms, and quantitates those transcripts.
It uses a novel network flow algorithm as well as an optional de novo assembly
step to assemble and quantitate full-length transcripts representing multiple
splice variants for each gene locus. Its input can include not only the alignments
of raw reads used by other transcript assemblers, but also alignments longer
sequences that have been assembled from those reads.In order to identify differentially
expressed genes between experiments, StringTie's output can be processed by specialized
software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).
Home : https://ccb.jhu.edu/software/stringtie
Manual : https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
Examples : https://ccb.jhu.edu/software/stringtie/index.shtml?t=example
The command line executable 'stringtie' of this module can be found in the folder:
The PATH is set to this folder, too.
Type 'stringtie' without any options to see the command-line parameters.
Examples for the usage on bwHPC clusters can be found in:
In case of problems, please contact 'firstname.lastname@example.org'.