vg rna pantranscriptome
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
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Jordan M Eizenga •
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z •
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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.