This dataset was processed with GL-DPPD-7101-A.
The raw and processed data are available from: https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-38/
These samples were processed in batch using the SLURM job scheduler. The following sub-directories contain the scripts used to generate each level of processed data.
- 00-RawData: Slurm scripts used to generate raw fastQC and multiQC reports
- 01-TG_PreProc: Slurm scripts used to generate trimmed reads, trimmed fastQC and multiQC reports
- 02-STAR_Alignment: Slurm scripts used to generate STAR reference and STAR alignment files
- 03-RSEM_Counts: Slurm scripts used to generate RSEM reference and RSEM count files
- 04-05-DESeq2_NormCounts_DGE: Slurm and R scripts used to generate raw and normlaized counts tables, differential gene expression (DGE), and DGE tables with annotations
| Program | Version | Relevant Links |
|---|---|---|
| FastQC | 0.11.8 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| MultiQC | 1.7 | https://multiqc.info/ |
| Cutadapt | 2.3 | https://cutadapt.readthedocs.io/en/stable/ |
| TrimGalore! | 0.6.2 | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| STAR | 2.7.1a | https://github.com/alexdobin/STAR |
| RSEM | 1.3.1 | https://github.com/deweylab/RSEM |
| Bioconductor | 3.9 | https://bioconductor.org |
| DESeq2 | 1.26.0 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| tximport | 1.14.0 | https://bioconductor.org/packages/release/bioc/html/tximport.html |
| tidyverse | 1.2.1 | https://www.tidyverse.org |
| STRINGdb | 1.24.0 | https://www.bioconductor.org/packages/release/bioc/html/STRINGdb.html |
| PANTHER.db | 1.0.4 | https://bioconductor.org/packages/release/data/annotation/html/PANTHER.db.html |
| org.At.tair.db | 3.8.2 | https://bioconductor.org/packages/release/data/annotation/html/org.At.tair.db.html |