Additional file 1 of BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data

Additional file 1. Various tables with information about BiocMAP inputs, outputs, test files, and more. This is provided as a multi-sheet excel file, with each sheet described in more detail below. S1: List of output metrics collected by BiocMAP. These are various quantities aggregated from processing steps like FastQC [15], trimming, alignment, and methylation extraction. Together they form an R data.frame accessible from the file metrics.rda and from within the colData() of output bsseq [11] objects. For paired-end samples, some metrics are computed separately for each mate, in which case metric names are appended with “_R1” and “_R2” to refer to each mate, respectively. S2: BiocMAP execution scripts and associated configuration files. BiocMAP provides several potential files for out-of-the-box functionality on local Linux machines as well as on SLURM or SGE-managed computing clusters. S3: Content of rules.txt. Each line of this input file to the extraction BiocMAP module consists of key-value pairs of the form $$ = $$ < k e y > = < v a l u e > , some of which are required. S4: Intermediate output files. These files are not the main output files of interest from running both modules of BiocMAP, but are generated along the way as byproducts. S5: Sources of test data provided in the BiocMAP repository. Human and mouse single-end and paired-end samples are provided to allow users to quickly verify proper installation of BiocMAP, sourced from SRA or the FlowRNA-WGBS dataset.