StringTie2
Quantify
- description
- Quantify gene expression using StringTie2.
Inputs
Required
aligned_bai(File, required): Aligned reads in BAI format.aligned_bam(File, required): Aligned reads in BAM format.gtf(File, required): Reference GTF file.
Optional
runtime_attr_override(RuntimeAttr?): Override default runtime attributes.
Defaults
keep_retained_introns(Boolean, default=false): Keep retained introns.prefix(String, default="out"): Prefix for output files.
Outputs
st_gtf(File)st_abund(File)
ExtractTranscriptSequences
- description
- Extract transcript sequences from a GTF file.
Inputs
Required
gtf(File, required): Reference GTF file.ref_fasta(File, required): Reference FASTA file.ref_fasta_fai(File, required): Reference FASTA index file.
Optional
runtime_attr_override(RuntimeAttr?): Override default runtime attributes.
Defaults
prefix(String, default="out"): Prefix for output files.
Outputs
transcripts_fa(File)transcripts_fai(File)transcripts_dict(File)
CompareTranscriptomes
- description
- Compare two GTF files.
Inputs
Required
guide_gtf(File, required): Reference GTF file.new_gtf(File, required): New GTF file.
Optional
runtime_attr_override(RuntimeAttr?): Override default runtime attributes.
Defaults
prefix(String, default="out"): Prefix for output files.
Outputs
annotated_gtf(File)loci(File)tracking(File)refmap(File)tmap(File)stats(File)