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
Parameter | Description | Defaultvalue |
---|---|---|
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 |
Parameters in Workflow File
Type: cufflinks
Parameter | Parameter in the GUI | Type |
---|---|---|
out-dir | Output directory | string |
ref-annotation | Reference annotation | string |
rabt-annotation | RABT annotation | string |
library-type | Library type | numeric |
mask-file | Mask file | string |
multi-read-correct | Multi-read correct | boolean |
min-isoform-fraction | Min isoform fraction | numeric |
frag-bias-correct | Frag bias correct | string |
pre-mrna-fraction | Pre-mRNA fraction | numeric |
path | Cufflinks tool path | string |
tmp-dir | Temporary directory | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input reads
Name in Workflow File: in-assembly
Slots:
Slot InGUI | Slot in Workflow File | Type |
---|---|---|
Assembly data | assembly | assembly |
Source url | url | string |
And 1 output port:
Name in GUI: Output annotations
Name in Workflow File: out-annotations
Slots:
Slot InGUI | Slot in Workflow File | Type |
---|---|---|
Isoform-level expression values | isolevel.slot | ann_table |