Screen shots of ExpressionPlot quality control tools. (a) read_types tool showing all read types. Numbers of non-aligning (Nonmatch), mulitply-aligning (Mult), unique genome-aligning (Genomic) and unique junction-aligning (Junction) reads are shown for each lane from a mouse tissue transcriptome dataset . Numbers (1/2) indicate different libraries; letters (A/B/C) indicate different lanes of the same library. (b) read_types tool showing matching read types, normalized to 100%. (c) Pairwise correlation heatmap of gene expression profiles generated from each lane. (d) pairdist tool shows ECDF of paired-end distances of 'canonical' reads (same chromosome, different strand, minus strand read downstream of plus strand read). 'Distance' is defined as the genomic distance, in nucleotides, between the aligned positions of the last sequenced bases of the two reads (can be negative if the alignments overlap). The samples have been de-identified (data in Additional file 3). Numbers in parentheses indicate median paired-end distance for each sample (add 36 for both sequences and 50 for both Illumina adaptors (+172) to get complete library size).