Genome files created by Mandy Waters - PepsiCo R&D
Track name: Illumina 6K unique probes	File: oat_6k_unique_probes.bed	Description: probe sequences from Illumina 6K array were mapped to the OT3098 genome using blast.  Blast hits were filtered so only probes with 1 exact hit (allowing 1 mismatch) were retained.  These probes are more likely to only pick up signal from one subgenome.
Track name: PepsiCo transcripts (PacBio)	File: oat_pep_transcripts_OT3098_95.gff3	Description: transcripts from PacBio data generated by PepsiCo were mapped to the OT3098 genome using GMAP.  Hits were then filtered for 95% coverage and 95% matches to ensure proper placement in the genome.  A transcript could map to multiple places (homoeologs) as long as the filtering criteria were met. Transcripts were not collaposed between the PepsiCo set and Hu et al set to facilite the user to visualize data from both sources.
Track name: Hu et al., 2019 transcripts (Illumina)	File: oat_hu_transcripts_OT3098_95.gff3	Description: transcripts from Hu et al., 2019 (https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13286) were mapped to the OT3098 genome using GMAP.  Hits were then filtered for 95% coverage and 95% matches to ensure proper placement in the genome.  A transcript could map to multiple places (homoeologs) as long as the filtering criteria were met. All proposed transcripts were mapped regardless of length. Transcripts were not collaposed between the PepsiCo set and Hu et al set to facilite the user to visualize data from both sources.