Galaxy |

StringTie merge (version 2.2.3+galaxy0)

Transcripts:

In GTF or GFF3 format

Reference annotation to include in the merging:

Minimum input transcript length to include in the merge:

Minimum input transcript coverage to include in the merge:

Minimum input transcript FPKM to include in the merge:

Minimum input transcript TPM to include in the merge:

Minimum isoform fraction:

Gap between transcripts to merge together:

Keep merged transcripts with retained introns:

By default these are not kept unless there is strong evidence for them

What it does?

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.