StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential 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.
Parameters in GUI
Use the reference annotation file (in GTF or GFF3 format) to guide the assembly process (-G).
The output will include expressed reference transcripts as well as any novel transcripts that are assembled.
Select the NGS libraries type: unstranded, stranded fr-secondstrand (--fr), or stranded fr-firststand (--rf).
Use the specified string as the prefix for the name of the output transcripts (-l).
|Min isoform fraction|
Specify the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus (-f).
Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts.
|Min assembled transcript length|
Specify the minimum length for the predicted transcripts (-m).
|Min anchor length for junctions|
Junctions that don't have spliced reads that align them with at least this amount of bases on both sides are filtered out (-a).
|Min junction coverage|
There should be at least this many spliced reads that align across a junction (-j).
This number can be fractional since some reads align in more than one place.
A read that aligns in n places will contribute 1/n to the junction coverage.
|Trim transcripts based on coverage|
By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript.
Set this parameter to "False" to disable the trimming at the ends of the assembled transcripts (-t).
|Min coverage for assembled transcripts|
Specifies the minimum read coverage allowed for the predicted transcripts (-c).
A transcript with a lower coverage than this value is not shown in the output.
This number can be fractional since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the coverage.
|Min locus gap separation|
Reads that are mapped closer than this distance are merged together in the same processing bundle (-g).
|Fraction covered by multi-hit reads|
Specify the maximum fraction of multiple-location-mapped reads that are allowed to be present at a given locus (-M).
A read that aligns in n places will contribute 1/n to the coverage.
|Skip assembling for sequences|
Ignore all read alignments (and thus do not attempt to perform transcript assembly) on the specified reference sequences (-x).
The value can be a single reference sequence name (e.g. "chrM") or a comma-delimited list of sequence names (e.g. "chrM,chrX,chrY").
This can speed up StringTie especially in the case of excluding the mitochondrial genome, whose genes may have very high coverage in some cases,
even though they may be of no interest for a particular RNA-Seq analysis.
The reference sequence names are case sensitive,
they must match identically the names of chromosomes/contigs of the target genome against which the RNA-Seq reads were aligned in the first place.
Enables or disables (-u) multi-mapping correction.
Enable detailed logging, if required (-v). The messages will be written to the UGENE log (enabling of "DETAILS" and "TRACE" logging may be required) and to the dashboard.
|Number of threads|
Specify the number of processing threads (CPUs) to use for transcript assembly (-p).
|Output transcripts file|
StringTie's primary output GTF file with assembled transcripts.
|Enable gene abundance output|
Select "True" to generate gene abundances output (-A). The output is written to a tab-delimited text file. Also, the file URL is passed to an output slot of the workflow element.
Parameters in Workflow File
|Parameter||Parameter in the GUI||Type|
Min isoform fraction
Min assembled transcript length
Min anchor length for junctions
Min junction coverage
Trim transcripts based on coverage
Min coverage for assembled transcripts
Min locus gap separation
Fraction covered by multi-hit reads
Skip assembling for sequences
Number of threads
Output transcripts file
Enable gene abundance output
The element has 1 input port:
Name in GUI: Input BAM file(s)
Name in Workflow File: in
|Slot in GUI||Slot in Workflow File||Type|
And 1 output port:
Name in GUI: StringTie output data
Name in Workflow File: out
|Slot in GUI||Slot in Workflow File||Type|