Workflows
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This workflow runs the FEELnc tool to annotate long non-coding RNAs. Before annotating these long non-coding RNAs, StringTie will be used to assemble the RNA-seq alignments into potential trancriptions. The gffread tool provides a genome annotation file in GTF format.
Tests This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.
This is part of a series of workflows to annotate a genome, tagged with TSI-annotation.
These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.
The workflows can be run in this order:
- Repeat masking
- RNAseq QC and read trimming
- Find transcripts
- Combine transcripts
- Extract transcripts
- Convert formats
- Fgenesh annotation
About this workflow:
- Inputs: multiple transcriptome.gtfs from different tissues, genome.fasta, coding_seqs.fasta, ...
This is part of a series of workflows to annotate a genome, tagged with TSI-annotation.
These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.
The workflows can be run in this order:
- Repeat masking
- RNAseq QC and read trimming
- Find transcripts
- Combine transcripts
- Extract transcripts
- Convert formats
- Fgenesh annotation
About this workflow:
- Run this workflow per tissue.
- Inputs: masked_genome.fasta and the trimmed RNAseq reads ...
ANNOTATO - Annotation workflow To Annotate Them Oll
Alignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.
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