StringTie

Reference

This is a special usage mode of StringTie, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts.

Category

Genome Annotation

Usage

stringtie <aligned_reads.bam> [options]*

Manual

-G   reference annotation to include in the merging (GTF/GFF3)
-o     output file name for the merged transcripts GTF(default: stdout)
-m     minimum input transcript length to include in the merge(default: 50)
-c     minimum input transcript coverage to include in the merge(default: 0)
-F    minimum input transcript FPKM to include in the merge(default: 1.0)
-T     minimum input transcript TPM to include in the merge(default: 1.0)
-f     minimum isoform fraction (default: 0.01)
-g     gap between transcripts to merge together (default: 250)
-i               keep merged transcripts with retained introns; by defaultthese are not kept unless there is strong evidence for them
-l

Protocols using this tool

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie

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