TSSAR: Transcription Start Site Annotation Regime Web Service
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