200602 - TRAIL/IZI in Melanoma
Principal investigators: Pr. Thomas Sauter (Luxembourg) / Pr. Dagmar Kulms (Dresden)
Data
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
Snakemake
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.yaml
main parameterssamples.tsv
sample annotationsunits.tsv
link samples and FASTQ files
Outputs
Main output is the DESeqDataSet
object from DESeq2
saved a binary file `deseq2/all.rds` after successful completion of the snakemake
pipeline.
Differential gene analysis and plots
See the file TRAIL_IZI.Rmd
, routines are loaded from R/utils.R
GeneWalk
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.
Tools used
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
- Constantin Ahlmann-Eltze, Peter Hickey and Hervé Pagès (2021). MatrixGenerics: S4 Generic Smmary Statistic Functions that Operate on Matrix-Like Objects. R package version 1.4.0. htps://bioconductor.org/packages/MatrixGenerics - Gu, Z. (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic dta. Bioinformatics. - H. Pagès, M. Lawrence and P. Aboyoun (2021). S4Vectors: Foundation of vector-like and list-like cntainers in Bioconductor. R package version 0.30.0. https://bioconductor.org/packages/S4Vectors - H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016. - Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for Common String Operations. R pckage version 1.4.0. https://CRAN.R-project.org/package=stringr - Hadley Wickham (2021). forcats: Tools for Working with Categorical Variables (Factors). R pckage version 0.5.1. https://CRAN.R-project.org/package=forcats - Hadley Wickham (2021). tidyr: Tidy Messy Data. R package version 1.1.3. htps://CRAN.R-project.org/package=tidyr - Hadley Wickham and Jim Hester (2020). readr: Read Rectangular Text Data. R package version 14.0. https://CRAN.R-project.org/package=readr - Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2021). dplyr: A Grammar of Data Mnipulation. R package version 1.0.7. https://CRAN.R-project.org/package=dplyr - Henrik Bengtsson (2021). matrixStats: Functions that Apply to Rows and Columns of Matrices (and t Vectors). R package version 0.59.0. https://CRAN.R-project.org/package=matrixStats - Jim Hester and Hadley Wickham (2021). vroom: Read and Write Rectangular Text Data Quickly. R pckage version 1.5.1. https://CRAN.R-project.org/package=vroom - Kamil Slowikowski (2021). ggrepel: Automatically Position Non-Overlapping Text Labels with 'gplot2'. R package version 0.9.1. https://CRAN.R-project.org/package=ggrepel - Kirill Müller and Hadley Wickham (2021). tibble: Simple Data Frames. R package version 3.1.2. htps://CRAN.R-project.org/package=tibble - Lawrence M, Huber W, Pag`es H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Anotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi:10.1371/journal.pcbi.1003118 - Lawrence M, Huber W, Pag`es H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi:10.1371/journal.pcbi.1003118 - Lionel Henry and Hadley Wickham (2020). purrr: Functional Programming Tools. R package version 03.4. https://CRAN.R-project.org/package=purrr - Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq dta with DESeq2 Genome Biology 15(12):550 (2014) - Martin Morgan, Valerie Obenchain, Jim Hester and Hervé Pagès (2021). SummarizedExperiment: SmmarizedExperiment container. R package version 1.22.0. htps://bioconductor.org/packages/SummarizedExperiment - Orchestrating high-throughput genomic analysis with Bioconductor. W. Huber, V.J. Carey, R. Gntleman, ..., M. Morgan Nature Methods, 2015:12, 115. - Orchestrating high-throughput genomic analysis with Bioconductor. W. Huber, V.J. Carey, R. Gntleman, ..., M. Morgan Nature Methods, 2015:12, 115. - R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Satistical Computing, Vienna, Austria. URL https://www.R-project.org/. - Sonali Arora, Martin Morgan, Marc Carlson and H. Pagès (2021). GenomeInfoDb: Utilities for mnipulating chromosome names, including modifying them to follow a particular naming style. R pckage version 1.28.0. https://bioconductor.org/packages/GenomeInfoDb - Wickham et al., (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686, https://doi.org/10.21105/joss.01686