Skip to end of metadata
Go to start of metadata

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

ParameterDescriptionDefaultvalue
Reference annotations

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.

 
Reads orientation

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

Unstranded
Label

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

STRG
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.

0.1

 

Min assembled transcript length

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

200
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).

10
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.

1
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).

True
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.

2.5

 

Min locus gap separation

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

50 bp
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.

0.95
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.

 
Multi-mapping correction

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

Enabled
Verbose log

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.

False
Number of threads

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

8
Output transcripts file

StringTie's primary output GTF file with assembled transcripts.

Auto
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.

False

Parameters in Workflow File

Type: stringtie

ParameterParameter in the GUIType

reference-annotations

Reference annotations

string

reads-orientation

Reads orientation

string

label

Label

string

min-isoform-fraction

Min isoform fraction

numeric

min-isoform-fraction

Min assembled transcript length

numeric

min-anchor-length

Min anchor length for junctions

numeric

min-junction-coverage

Min junction coverage

numeric

trim-transcripts

Trim transcripts based on coverage

bool

min-coverage

Min coverage for assembled transcripts

numeric

min-locus-gap

Min locus gap separation

numeric

multi-hit-fraction

Fraction covered by multi-hit reads

numeric

skip-sequences

Skip assembling for sequences

string

multi-mapping-correction

Multi-mapping correction

bool

verbose-log

Verbose log

bool 

threads

Number of threads

numeric

transcripts-output-url

Output transcripts file

string

gene-abundance-output

Enable gene abundance output

bool

Input/Output Ports

The element has 1 input port:

Name in GUI: Input BAM file(s)

Name in Workflow File: in

Slots:

Slot in GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: StringTie output data

Name in Workflow File: out

Slots:

Slot in GUISlot in Workflow FileType
Output URLurlstring
  • No labels