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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).

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

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

Junctions that don't have spliced reads that align them with at least this amount of bases on both sides are filtered out (-a).

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.

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).

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

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

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.

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