vg rna with pggb gfa file

[agolicz]

Hi, I am trying to add annotation to my graph built using pggb, but I can't seem to see the corresponding paths. I assume I must be doing something wrong.

My commands are as follows: pggb -i Cvi.Ler.chr1.fasta -s 100000 -p 90 -n 2 -t 20 -o out2 (completes without issues)

vg paths -L -v out2/Cvi.Ler.chr1.fasta.a944863.34ee7b1.891e76b.smooth.gfa Cvi.chr1 Ler.chr1

head -n 2 Cvi.chr1.gtf Cvi.chr1 EVM transcript 2621 4479 . + . transcript_id "ATCVI-1G10010.1"; gene_id "ATCVI-1G10010"; Cvi.chr1 EVM exon 2621 2774 . + . transcript_id "ATCVI-1G10010.1"; gene_id "ATCVI-1G10010";

head -n 2 Ler.chr1.gtf Ler.chr1 EVM transcript 2676 4546 . + . transcript_id "ATLER-1G10010.1"; gene_id "ATLER-1G10010"; Ler.chr1 EVM exon 2676 2829 . + . transcript_id "ATLER-1G10010.1"; gene_id "ATLER-1G10010";

vg rna -n Cvi.chr1.gtf -n Ler.chr1.gtf out2/Cvi.Ler.chr1.fasta.a944863.34ee7b1.891e76b.smooth.gfa > test.annot.gfa (completes without issues)

vg paths -L -v test.annot.gfa Cvi.chr1 Ler.chr1

So not paths get added. I had the same issue with annotate/augment. Any chance you could point me in the right direction?

Best, Agnieszka

[jonassibbesen]

Hi Agnieszka,

Transcript paths are not added to the graph by default in vg rna (only splice-junctions are). You can add the paths to the graph using the option -r. You can find more information on vg rna in the Transcriptomic analyses wiki (https://github.com/vgteam/vg/wiki/Transcriptomic-analyses).

Best,

Jonas