rice.bg: Rice ballgown object

In VaSP: Quantification and Visualization of Variations of Splicing in Population

Description

Small ballgown object created with a subset of rice RNAseq data, for demonstration purposes

Format

a ballgown object with 33 transcripts and 6 samples

Details

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 rice.bg is a subset ballgown object with 33 transcripts and 6 samples (Yu et al., 2021).

Source

The raw RNA-seq data were from the project of variation in transcriptional responses to salt stress in rice (SRA Accession: SRP106054)

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.

Examples

data(rice.bg)
rice.bg
# ballgown instance with 33 transcripts and 6 samples

VaSP documentation built on Feb. 28, 2021, 2:02 a.m.