dudududu12138

> It would be great if we could do this, but it causes a lot of trouble for the parallel-by-contig, streaming architecture we use in the constructor. So I think...

By the way, can I just construct a spliced reference graph? There are no variants in this graph, just spliced nodes. I just provide the reference(.fa) and the annotation file(.gff)....

> You may find this script useful https://github.com/broadinstitute/SpliceAI-lookup/blob/master/annotations/convert_gtf_to_SpliceAI_annotation_input_format.py It's used for updating the annotations that underly https://spliceailookup.broadinstitute.org/ > […](#) > On Tue, Jan 2, 2024, 7:10 AM dudududu12138 ***@***.***> wrote:...

By the way, I use the [gbz](https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-grch38/hprc-v1.1-mc-grch38.d9.gbz) file and the `.xg` file of Minigraph Cactus graph to running `vg pack` and `vg call`, and I got 2 vcf files. I...

I got the same result and my iupred2a result is not null. So do you know the solution？

> Hi, > > You are correct that ncore mainly speeds up the performance when running multiple samples as we distribute each sample to a different core for read class...

Hi, I have figured out why the two transcripts have the same `tssid`, but the transcription start sites are far apart. You set a cutoff to cluster transcript start site(`-d`...