The RNA-Seq FASTQ files obtained after Ion Proton sequencing were mapped using TopHat2 (version 2.1.1) [Kim2013], with default settings and using additional transcript annotation data for the hp19 genome from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). According to the Ion Proton manufacturers recommendation, the reads which remained unmapped were submitted to a second round of mapping using Bowtie2 (version 2.2.8) [Langmead2012] against the hp19 genome with the --very-sensitive switch turned on and merged with the initial mappings. The alignments of technical replicates were merged using samtools [Li2009].

[Kim2013] Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. . Genome Biology 2013, 14:R36
[Langmead2012] Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
[Li2009]  Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9.