The extdata directory contains:

1. Three .bam files and the corresponding index files;
2. Six directories of expression information of 6 samples and 33 transcripts.

Source

The raw RNA-seq data were from the project of variation in transcriptional 
responses to salt stress in rice (SRA Accession: 
SRP106054<https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP106054>)


Processing

The raw RNA-seq data were screened and trimmed using Trimmomatic 
(Bolger et al., 2014) and RNA-seq mapping, transcript assembly, and 
quantification were conducted with HISAT, StringTie, and Ballgown by 
following the method described by Pertea et al. (Pertea et al., 2016). The 3 
.bam files and the corresponding index files were ouput from HISAT2 mapping and 
the 6 directories of expression information were ouput from StringTie. 
The dataset rice.bg was a subset of Ballgown with 33 transcripts and 6 samples.
See ?rice.bg for details.


References

Yu, H., Du, Q., Campbell, M., Yu, B., Walia, H. and Zhang, C. (2021), Genome‐wide discovery of natural variation in pre‐mRNA splicing and prioritising causal alternative splicing to salt stress response in rice. New Phytol. https://doi.org/10.1111/nph.17189

Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible 
trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120.
 
Pertea, M., Kim, D., Pertea, G.M., Leek, J.T., and Salzberg, S.L. (2016). 
Transcript-level expression analysis of RNA-seq experiments with HISAT, 
StringTie and Ballgown. Nat Protoc 11, 1650-1667.
