Entering edit mode
3 months ago
Juhyun
•
0
Hi developer,
I have a quick and very ambiguous question regarding transcriptome graph analysis. Is there any way to extract or retrieve the projected(liftover) transcriptome annotation in a graph from reference annotation to each haplotype, formatted in GTF or another format based on haplotype coordinates?
My graph was generated using the command below:
vg rna -p --threads $SLURM_CPUS_PER_TASK \
-q \
--transcripts ${wd}/03.pantranscriptome/${chr}.gtf --gbz-format \
--write-gbwt ${wd}/03.pantranscriptome/${chr}.pantranscriptome.gbwt \
--write-info ${wd}/03.pantranscriptome/${chr}.pantranscriptome.txt \
-f ${wd}/03.pantranscriptome/${chr}.pantranscriptome.fa \
${wd}/02.minigraph-cactus/${prefix}.${chr}.gbz \
> ${wd}/03.pantranscriptome/${chr}.spliced_graph.pg
The "--proj-embed-paths" parameter inspired me this idea. If you have any possible way to do that, please let me know. \ it would be very helpful to me! : )
Thanks,\ Jh
In principle, it wouldn't be hard to do that, but this feature is not currently implemented in
vg
. You could consider opening a feature request on thevg
GitHub page if this is something that would be important for your research.