Computational protocol: Fundamental Roles of the Golgi-Associated Toxoplasma Aspartyl Protease, ASP5, at the Host-Parasite Interface

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Protocol publication

[…] RNA Sequencing was performed on the Illumina HiSeq 2500 at the iGE3 genomics plateform of the University of Geneva (http://www.ige3.unige.ch/genomics-platform.php). The adapter sequences from the raw reads obtained from the RNA-Seq were trimmed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) (phred<20). The resulting reads, after quality control, were aligned to the latest mouse reference genome (GRCm38) using TopHat/Bowtie2 aligner and HTSeq-count was used to get the read counts of the genes [–]. Differential expression analysis was carried out using edgeR, a Bioconductor package in R (http://www.R-project.org). Normalized expression values from the count data were obtained from the normalization factors calculated by the TMM (trimmed mean of the M values) method. The heatmaps for the genes of interest were also generated in R using heatmap.2 in the gplots package. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis was performed using KOBAS 2.0 (KEGG Orthology Based Annotation System) [, ]. All the computations were performed at University of Geneva on the Baobab cluster. […]

Pipeline specifications

Software tools FASTX-Toolkit, TopHat, Bowtie2, HTSeq, edgeR, gplots, KOBAS
Databases KEGG
Application RNA-seq analysis
Organisms Toxoplasma gondii