vg rna pantranscriptome
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9 months ago
z • 0

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

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

rna vg • 564 views
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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.

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