Principal investigators: Pr. Thomas Sauter (Luxembourg) / Pr. Dagmar Kulms (Dresden)
Experimenter: Sebastian Schindler (Dresden)
Sequencing on total RNA: Rashi Halder (Luxembourg)
24 FASTQ generated (deposited in ArrayExpress E-MTAB-10669)
10-1-Lasse_S10_R1_001.fastq.gz
10-3-Lasse_S16_R1_001.fastq.gz
11-1-Lasse_S11_R1_001.fastq.gz
11-3-Lasse_S17_R1_001.fastq.gz
1-1-Lasse_S1_R1_001.fastq.gz
12-1-Lasse_S12_R1_001.fastq.gz
12-3-Lasse_S18_R1_001.fastq.gz
1-3-Lasse_S7_R1_001.fastq.gz
2-1-Lasse_S2_R1_001.fastq.gz
2-3-Lasse_S8_R1_001.fastq.gz
3-1-Lasse_S3_R1_001.fastq.gz
3-3-Lasse_S9_R1_001.fastq.gz
4-1-Lasse_S4_R1_001.fastq.gz
4-3-Lasse_S10_R1_001.fastq.gz
5-1-Lasse_S5_R1_001.fastq.gz
5-3-Lasse_S11_R1_001.fastq.gz
6-1-Lasse_S6_R1_001.fastq.gz
6-3-Lasse_S12_R1_001.fastq.gz
7-1-Lasse_S7_R1_001.fastq.gz
7-3-Lasse_S13_R1_001.fastq.gz
8-1-Lasse_S8_R1_001.fastq.gz
8-3-Lasse_S14_R1_001.fastq.gz
9-1-Lasse_S9_R1_001.fastq.gz
9-3-Lasse_S15_R1_001.fastq.gz
The quality controls, read trimming, feature counting were performed using Snakemake and the tailor-made RNA-seq template.
The 3 config files are provided in the config folder:
config.yamlmain parameterssamples.tsvsample annotationsunits.tsvlink samples and FASTQ files
Main output is the DESeqDataSet object from DESeq2 saved a binary file `deseq2/all.rds` after successful completion of the snakemake pipeline.
See the file TRAIL_IZI.Rmd, routines are loaded from R/utils.R
Performed on 1,248 genes using the BASH script run_genewalk.sh on the https://hpc.uni.lu iris machine.
The input file same_pdirection.txt is also part of this repository.
The experiments presented in this paper were carried out using the HPC facilities of the University of Luxembourg (Varrette et al. 2014, https://hpc.uni.lu).
Varrette S., Bouvry P., Cartiaux H. and Georgatos F. Management of an Academic HPC Cluster: The UL Experience. Proc. of the 2014 Intl. Conf. on High Performance Computing & Simulation. HPCS 2014. 959-967.
| software and algorithms | source | product number/identifier |
|---|---|---|
| AdapterRemoval | https://github.com/MikkelSchubert/adapterremoval | v2.3.1 |
| apeglm | R bioconductor | v1.10.0 |
| ComplexHeatmap | https://github.com/jokergoo/ComplexHeatmaps | v2.7.8.1000 |
| DESeq2 | R bioconductor | v1.128.1 |
| FALCON | De Landtsheer et al. 2017, https://github.com/sysbiolux/FALCON | |
| GeneWalk | Ietswaart et al. 2021, https://churchman.med.harvard.edu/genewalk | v1.5.1 |
| ggplot2 | R CRAN | v3.3.2 |
| ggVennDiagram | R CRAN | v1.1 |
| ggforce | R CRAN | v0.3.3 |
| multiqc | https://multiqc.info/ | v1.9 |
| python | https://python.org/ | v3.8.2 |
| R Project for Statistical Computing | https://www.r-project.org | v4.0.0 |
| RStudio | https://www.rstudio.com/ | v1.0.143 |
| Rsubread | R bioconductor | v2.2.2 |
| SAMtools | https://www.htslib.org | v1.10 |
| Snakemake | https://snakemake.github.io | v5.20.1 |
| STAR | https://github.com/alexdobin/STAR | v2.7.4a |
| Tidyverse | R CRAN, http://tidyverse.org/ | v1.1.1 |
Tools citation
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