(a) Histogram of inferred insert size for each sample, which represents distance between the two reads of one RNA fragment. (b) Principle component analyses (PCA) plots were performed to assess variability of samples within and between groups. Plot of the first two axes from a PCA based on the 500 genes with the most variable expression across all samples except MDX_1. CASK control (red, n=3) and KO (green, n=3); MDX control (orange, n=5) and KO (blue, n=4); SAP97 control (grey, n=3) and KO (black, n=3). (c) Distribution of GC content of the reads for each sample. (d) Base quality (Phred scores) along the length of the reads in each FastQC file of MDX_Ct1 as representative sample. The box plots are drawn as follows: red line, median; yellow box, range between upper and lower quartiles; whiskers, range between 10 and 90% quantiles. The blue line shows the mean quality. Y-axis represents quality scores across all bases. X-axis represents position in read (bp). (e) Gene body coverage. Distribution of reads along the length of the genes (5’-end on the left, 3’-end on the right). Shown image of sample MDX_Ct1 is representative for all samples. (f) Saturation report, depicting the number of splice junctions detected using different subsets of the data from 5 to 100% of all reads. Red, known junction based on the provided genome annotation; green, novel junctions; blue, all junctions. The red line reaches a plateau where adding more data does not increase the number of detected junctions, indicating that the sequencing depth suffices for performing alternative splicing analysis.