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Figure 1 | BMC Bioinformatics

Figure 1

From: TSSAR: TSS annotation regime for dRNA-seq data

Figure 1

Post-processing and Visualization. (A) Similar, but more restrictive, to the scheme in [4] each annotated transcription start site is classified according to its genomic context: If a TSS is positioned within 250 nt upstream of an annotated gene, it is classified as Primary. TSS within an annotated gene is labeled Internal. A TSS which is on the opposite strand of an annotated gene is classified as Antisense. This class further splits into Ai and Ad, for internal antisense and downstream antisense, respectively. The latter is reserved for a TSS which points in the opposite reading direction and is less than 30 nt downstream of an annotated gene. A TSS that falls in none of these classes is reported to be Orphan. (B) As a matter of fact, one TSS can have several labels as it might fall into more than one of the aforementioned classes. The TSSAR Web service summarizes the counts of the overlapping main classes graphically. (C) For TSS which are annotated as ’Primary’ the 5’UTR lengths are deduced and the corresponding distribution is plotted. (D) To assess the efficiency of the TEX treatment, the distribution of read starts per position is provided as a helpful indicator. If the enrichment in the [+]-library worked efficiently, we expect fewer read start sites, each of which will have more reads. Hence the distribution is flattened on the left side and bulged at the right side. The corresponding distribution and the mean (dashed line) is expected to be shifted to the right compared to the [–]-library.

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