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Protocol publication

[…] RNA-sequencing was performed with strand-specific TruSeq libraries on an Illumina HiSeq High Output Mode with paired-end 50 bp reads. Quality control of raw read files was performed with FastQC (0.11.2). Adapters and low quality reads were removed with Trimmomatic (0.32), and the remaining reads were aligned to the Human GRCh38 reference genome with Star (2.4.1 c), with default parameters. Read counts per exonic region were extracted with the featureCounts (1.5.0) R package using the Homo_sapiens.GRCh38.83.gtf file as reference annotation. MultiQC (0.3.1) was used to aggregate results from multiple samples. Differential expression analysis was performed with the edgeR-__STRONG_START__Limma (3.24.15) pipeline, using the read count table as input and filtering genes that were lowly expressed. After the comparisons, genes were considered as statistically up- or down-regulated based on Benjamini-Hochberg-corrected p-values with a cutoff of 5%. Analysis of RNA-sequencing reads was performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), with support by Bioinformatics Infrastructure for Life Sciences (BILS). […]

Pipeline specifications

Software tools FastQC, Trimmomatic, Subread, MultiQC, edgeR, limma
Application RNA-seq analysis
Diseases Infection, Malaria, Malaria, Falciparum