vg rna pantranscriptome

Question

[z]

Hello,VG team. I have assembled my pan-transcriptome according to this technical route.

Is this approach feasible if I build a Haplotype-aware pantranscriptome using the pan-transcriptome and a haplotype vcf file generated by standard reference genome ? It is known that these transcripts generated from unmap-reads that do not have their any information in the haplotype vcf file and the standard reference genome. Thanks

[Jordan M Eizenga]

Yes, you can use a set of annotations in GTF format and a phased VCF file to produce a pantranscriptome. It seems like this is primarily a pipeline to construct the annotations, which is a somewhat separate matter. I can't really speak to whether this is a reasonable annotation pipeline, but you should be able to use the output for pantranscriptome construction.