improve annotations

[sqwwww]

Ask away!

I have an annotation gff file generated from illumina RNA data， now I want to improve my annotation using the ont isoseq data (ie, correct wrong gene structure, find new genes and new transcripts).

I noticed that this pipeline can improve the annotation in the documentation. however, I didn't find the improved gff annotation in the result. My question is: how can I get an improved genome annotation from current result file? I found there was a "merged_transcriptome.fas", probably I can generated an improved annotation from this transcriptome sequence file？

here is my command：

nextflow -c nextflow.config run epi2me-labs/wf-transcriptomes \
--fastq $input_fq \
--ref_genome $ref_fa \
--transcriptome-source reference-guided \
--ref_annotation $ref_gff \
--minimap2_index_opts '-k 15'  \
-profile singularity \
-resume 49c68a8e-919d-4f48-aee4-e6ddc01c4604

[sarahjeeeze]

Hi, could you clarify are you looking for an improved gff/gtf annotation file in the output? The workflow doesn't provide this unfortunately, maybe we need to reword the documentation

[sarahjeeeze]

Closing through lack of response.