Assemble Transcripts with StringTie Element

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.

reference-annotations

string

Select the NGS libraries type: unstranded, stranded fr-secondstrand (--fr), or stranded fr-firststand (--rf).

reads-orientation

string

Use the specified string as the prefix for the name of the output transcripts (-l).

label

string

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.

0.1

min-isoform-fraction

numeric

Specify the minimum length for the predicted transcripts (-m).

min-isoform-fraction

numeric

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-anchor-length

numeric

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.

min-junction-coverage

numeric

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).

trim-transcripts

bool

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.

2.5

min-coverage

numeric

Reads that are mapped closer than this distance are merged together in the same processing bundle (-g).

min-locus-gap

numeric

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.

multi-hit-fraction

numeric

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.

skip-sequences

string

Enables or disables (-u) multi-mapping correction.

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.

verbose-log

bool 

Specify the number of processing threads (CPUs) to use for transcript assembly (-p).

threads

StringTie's primary output GTF file with assembled transcripts.

transcripts-output-url

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.

gene-abundance-output