Adding gene annotations in spliced_bam2gff

nanoporetech / pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish

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Adding gene annotations in spliced_bam2gff #8

Closed mvemulap closed 5 years ago

mvemulap commented 5 years ago

Hello,

Can you let me know how to add the gene annotations to the gff file produced by spliced_bam2gff. My output file (raw_transcripts.gff) contains read names in the gene id and transcript id columns.

I am declaring the file to be used in config.yaml: genome_annot: "/pathto/ReferenceData/Homo_sapiens.GRCh38.97.gff3.gz"

Please let me know if I need to change anything or if I am missing something.

Thanks, Meg

bsipos commented 5 years ago

The pinfish pipeline does not use prior annotation at all, hence the IDs have no relation to existing annotation. If you want to "match up" transcripts from the pipeline with the existing annotation you will have to use the gffcompare tool.

mvemulap commented 5 years ago

Got it ! Thanks so much!