Barley RTD
- Barley Reference Transcript (BaRTv2.18) Dataset
Introduction
BaRTv2.18 is based on parallel Iso-seq and Illumina RNA-seq of the same diverse set of samples from barley cultivar Barke. We have developed novel methods of Iso-seq analysis for accurate determination of splice junctions (SJs) and transcription start and end sites (TSS/TES). These methods overcome issues of false SJ calling due to sequencing errors and distinguishing TSS/TES from transcript fragments due to degradation. We apply a new program, RTDmaker, for quality control of Illumina short read assemblies and the merging of Iso-seq and Illumina data. We also use TranSuite, a program for defining “true” translations and transcript characteristics.
| Description | Download File |
|---|---|
| The BaRTv2.18 fasta file of transcript sequences. Use this with salmon/kallisto for transcript/gene resolution RNA-seq quantification | BaRT2v18.fa.gz |
| The gtf file of transcript coordinates including CDS information annotated from transfix. | BaRT2v18_transfix.gtf.gz |
| The fasta file of predicted peptide sequences for BaRTv2.18. | BaRT2v18_transfix_pep.fasta.gz |
| The tab delimited table of transcript-by-transcript information, including location, source data, feature locations, coding potentiality, predicted functions, GO ids etc. | BaRT2v18_annotation.txt.gz |