For a given RNA, SHAPE-MaP involves the generation of sequencing data for RNA treated under three distinct experimental conditions: plus-reagent, minus-reagent and denaturing control. For input into ShapeMapper, these samples can either be sequenced separately or sequenced together and deconvoluted using multiplexed barcodes (such as Illumina TruSeq). Sequencing reads should be output as FASTQ files; this format is widely available with modern sequencing platforms. 对于给定的RNA，SHAPE-MaP涉及为在三种不同实验条件下处理的RNA生成测序数据：加试剂、减试剂和变性对照。为了输入到ShapeMapper中，这些样本可以单独测序，也可以一起测序并使用多路复用条形码（如Illumina TruSeq）进行去卷积。排序读数应输出为 FASTQ 文件;这种格式在现代测序平台上广泛使用。