Overview of the classification of putative TSSs within the
MGA3 genome sequence. (A) Schematic illustration of the different categories which were used for the classification of TSSs based on the respective genomic context. Putative TSSs are depicted as angled black arrows and are identified as described in section “Preparation of two different cDNA libraries for high-throughput sequencing” using the read starts obtained from RNA-seq data of enriched 5′-ends cDNA library. TSSs located in the upstream region and in coding direction of known CDSs (gray arrows) were classified as single TSSs or multiple TSSs. All TSSs overlapping in sense direction with known CDSs were categorized as novel intragenic TSSs. TSSs without annotated features downstream were classified as novel intergenic TSSs (black arrow), while TSSs antisense to annotated CDSs were classified as novel antisense TSSs (black arrow). (B) Process of TSSs analysis which includes the identification, filtering, manual verification and classification of putative TSSs. After manual inspection TSSs that belong to rRNA/tRNA and false-positive TSSs were removed from the automatically detected set, whereas the manually detected TSSs were added. The complete set of verified TSSs was divided into subsets depending on their genomic context.