### Simulated reads

This folder contains paired-end RNA-seq reads simulated using vg sim (https://github.com/vgteam/vg). The reads were simulated from HG002 haplotype-specific transcripts using an uniform expression profile. “_h1” and “_h2” denote which haplotype the data was simulated from. 

The "graph" subfolder contains the spliced pangenome graph and the haplotype-specific transcripts that were used to generate the simulated data.

File types:

 “.fq.gz”: Simulated RNA-seq reads.

 “.gam”: True graph alignments for the simulated RNA-seq reads.

 “.txt.gz”: Table with the true transcript path and position for each simulated RNA-seq read.

 “.bam”: Alignments of the HG002 haplotype-specific transcripts to GRCh38.

Updates:

* 25/01/2023: Added graph subfolder

* 25/10/2022: Updated simulated data to the newest version

* 04/07/2022: Added simulated reads