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TSSAR: Transcription Start Site Annotation Regime Web Service

TSSAR predicts bacterial Transcription Start Sites based on dRNA-seq data and a statistical model. A typical TSSAR run produces several output files wich are explained below.

TSSAR Output explained

Predicted TSS

A list of all genomic positions which full fill the cutoff requirements specified by the user.
Available as BED, GFF, CSV, TSV, XLSX

Predicted TSS (merged)

A list of annotated TSS after consecutive significant positions were merged together (the maximal range to call two positions consecutive are defined by the user via the merge range parameter).
Available as BED, GFF, CSV, TSV, XLSX

TSS classification

If a reference genome was specified, each annotated TSS is classified with respect to its genomic context. Therefore the classes 'primary' (up to 250 nt upstream of annotated gene), 'internal' (within an annotated gene), 'anti-sense' (on the opposite strand to an annotated gene), and 'orphan' (everything else) are coined.
Available only if reference genome was specified as BED, GFF, CSV, TSV, XLSX

Dumped Regions

Regions where the applied zero-inflated Poisson regression does not converge are omitted from the analysis and need manual inspection. Therefore, all regions which were omitted are provided in the BED file dump.bed. Users are strongly encouraged to manually check the pattern of mapped reads within this region manually. It is important to emphasize that TSSAR does not say positions in the dumped regions are not significant TSS, but the algorithm explicitly says nothing about this positions. So please check manually.

Read Start Distribution

o 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.
Available as SVG and PNG

Distance Histogram

For all positions which are classified as Primary TSS the distance to the closest translation start is calculated. Thereof a histogram with the distribution of 5' utr length is porvided.
Available only if reference genome was specified as SVG and PNG

Venn Diagram

The number of TSS classified as primary, secondary and anti-sense are provided in the form of an Venn diagram. Please note that TSS clasified as orphan are omitted.
Available only if reference genome was specified as SVG and PNG

If TSSAR is useful for your work or if you use any figures or data procuced by TSSAR, please cite the original TSSAR publication: "TSSAR: TSS Annotation Regime for dRNA-seq data" F. Amman, M.T. Wolfinger, R. Lorenz, I.L. Hofacker, P.F. Stadler and S. Findeiß BMC Bioinformatics 2014 15:89 doi:10.1186/1471-2105-15-89 - Contact: