Similar protocols

Protocol publication

[…] Fastq files were mapped to the chicken genome galGal4 from UCSC using Tophat (2.0.13) with options -x 1 g 1. Ensembl 80 annotations were used to define gene coordinates. Quality of the samples was assessed using FastQC (0.10.1). The R environment (RRID:SCR_001905) was used for the statistical analysis of the data. All annotated code is located in . RPKM values generated and differentially expressed genes were found using edgeR. Genes were considered differentially expressed if they had an Benjamini-Hochberg adjusted p-value less than 0.05 and a log2 fold change greater than 2 or less than −2. Hierarchical clustering was performed using Pearson correlations. Clustering was achieved using base principal component functions in R. Gene ontology (GO) analysis was completed using ClusterProfiler (3.2.6). GO terms with a p value less than 0.05 and a q value below 0.1 were considered significant. Significant GO terms were condensed using the simplify function with an adjusted p value cutoff of 0.05. Pathway enrichment analyses were performed using Qiagen’s Ingenuity Pathway Analysis (RRID:SCR_008653; v31813283, Hilden, Germany). […]

Pipeline specifications

Software tools TopHat, FastQC, edgeR, clusterProfiler, IPA
Application Genome annotation
Organisms Caenorhabditis elegans, Gallus gallus