Fig. 2

BEAVR requires two inputs: a read count table file and a sample treatment matrix file. aBEAVR requires raw, unnormalized read counts as input. This can be obtained using tools such as STAR or HTSeq. The first column of the read count table file must have the heading gene_id and contain unique ENSEMBL IDs. Every column after must contain read counts for one sample, each with a unique identifier in the heading (e.g. Sample-1, Sample-2, …, Sample-n). The read count table file must be either a TXT or CSV format. bBEAVR requires an additional file, called a sample treatment matrix file, that contains characteristics about each sample, such as which treatment group the samples belong to. The first column of this file must contain in each row all the samples found in the read count table file (e.g. Sample-1, Sample-2, …, Sample-n) in the same order. The second column must have the heading condition. The third column must have the heading replicate. In the condition column, users must specify which experimental group each sample belongs to (e.g. Wildtype, Mutant, or Drug-Treated). In the replicate column, users can provide any other additional grouping information or replicate information (e.g. Replicate-1, Replicate-2, …, Replicate-n). The sample treatment matrix file must be either a TXT or CSV format