Additional file 3 of SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

Additional file 3: Table S1. Available configuration profiles. Configuration files exist under the SPEAQeasy/conf directory. Configuration profiles exist for SGE and SLURM clusters, as well as local execution on a Linux machine. These profiles can be customized for specific clusters, such as the JHPCE configuration file jhpce.config, which runs on an SGE cluster. The file a user chooses also depends on whether software dependencies are managed with docker, or are installed locally. Table S2. SPEAQeasy output files. Table of intermediary outputs generated by SPEAQeasy. These do not include the major output files of interest (Fig. 2), but other miscellaneous outputs from each processing step. In the Filename column, brackets denote one or more values dependent on a relevant variable; for example, the files [sample_name]_process_trace.log refer to a set of several files, each named distinctly according to the sample associated with the particular file. An asterisk represents a wildcard matching more than one file, when individual file names may depend on the experiment. For example, [sample_name]_trimmed*.fastq could refer to sample1_trimmed_1.fastq and sample1_trimmed_2.fastq. The next columns provide the directory containing each given file, relative to the output folder, and a description of the files’ content, respectively. Table S3. Quality metrics recorded in SPEAQeasy outputs. One of the major pipeline outputs is a comma-separated values (CSV) file where fields (columns) are different quality metrics, and each line (row) is associated with one sample. A list of the exact field names and their descriptions is given above. Table S4. SPEAQeasy-example differential expression and gene ontology results. (A) Differential expression results using the subset of BipSeq data analyzed in http://research.libd.org/SPEAQeasy-example/ . (B) Gene ontology enrichment results from the genes with a p-value