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

附加文件3：表S1 可用配置方案。配置文件存放于SPEAQeasy/conf目录下，提供适配SGE、SLURM集群以及Linux本地运行的配置方案。此类方案可针对特定集群进行自定义调整，例如适配SGE集群的JHPCE配置文件jhpce.config。用户所选配置文件需结合软件依赖的管理方式（Docker容器化部署或本地手动安装）进行选择。

表S2：SPEAQeasy输出文件。该表汇总了SPEAQeasy生成的中间输出结果，未包含核心目标输出文件（见图2），仅涵盖各处理步骤产生的各类杂项输出。文件名列中的方括号代表一个或多个由相关变量决定的取值；例如，[sample_name]_process_trace.log 指代一组文件，每个文件的名称均根据其关联的样本进行个性化命名。星号则代表通配符，可匹配多个因实验设计而异的文件；例如，[sample_name]_trimmed*.fastq 可指代sample1_trimmed_1.fastq与sample1_trimmed_2.fastq这类文件。后续两列分别列出了各文件相对于输出目录的存放路径，以及文件内容的详细说明。

表S3：SPEAQeasy输出结果中记录的质量指标。该分析流程的核心输出之一为逗号分隔值（CSV）格式文件，其中列字段为各类质量指标，每一行对应一个样本。各字段的准确名称与含义已在前文给出。

表S4：SPEAQeasy示例差异表达与基因本体论分析结果。(A) 基于http://research.libd.org/SPEAQeasy-example/ 中分析的BipSeq数据子集得到的差异表达分析结果；(B) 基于p值筛选的基因所得到的基因本体论富集分析结果。