Output

Master Table (MasterTable.tsv)

This table contains information on positions and class assignments of all automatically annotated TSS. The table consists of the following columns:

SuperPos The position of the TSS in the SuperGenome.

SuperStrand The strand of the TSS in the SuperGenome.

MapCount Number of strains into which the TSS can be mapped. Separate entry lines exist for each strain to which the TSS can be mapped whether the TSS was detected in that strain or not.

detCount The number of strains/conditions in which this TSS was detected in the RNA-seq data.

Condition The identifier of the strain/condition to which the rest of the line relates.

detected Contains a ‘1’ if the TSS was detected in this strain/condition.

enriched Contains a ‘1’ if the TSS is enriched in this strain/condition.

stepHeight The expression height change at the position of the TSS. This relates to the number of reads starting at this position. (e(i) - e(i-1); e(i): expression height at position i)

stepFactor The factor of height change at the position of the TSS. (e(i)/e(i-1); e(i): expression height at position i)

enrichmentFactor The enrichment factor at the position of the TSS.

classCount The number of classes to which this TSS was assigned.

Pos Position of the TSS in that genome.

Strand Strand of the TSS in that genome.

Locus tag The locus tag of the gene to which the classification relates.

Product The product description of this gene.

UTRlength The length of the untranslated region between the TSS and the respective gene (nt). (Only applies to ‘primary’ and ‘secondary’ TSS.)

GeneLength The length of the gene (nt).

Primary Contains a ‘1’ if the TSS was classified as ‘primary’ with respect to the gene stated in ‘locusTag’.

Secondary Contains a ‘1’ if the TSS was classified as ‘secondary’ with respect to the gene stated in ‘locusTag’.

Internal Contains a ‘1’ if the TSS was classified as ‘internal’ with respect to the gene stated in ‘locusTag’.

Antisense Contains a ‘1’ if the TSS was classified as ‘antisense’ with respect to the gene stated in ‘locusTag’.

Automated Contains a ‘1’ if the TSS was detected automatically.

Manual Contains a ‘1’ if the TSS was annotated manually.

Putative sRNA Contains a ‘1’ if the TSS might be related to a novel sRNA. (Not evaluated automatically)

Putative asRNA Contains a ‘1’ if the TSS might be related to an asRNA.

Sequence -50 nt upstream + TSS (51nt) Contains the base of the TSS and the 50 nucleotides upstream of the TSS.

Supplemental Files

*strain* _super.fa Contains the genome sequence of each strain mapped to the coordinate system of the SuperGenome. All 4 files together actually contain the whole-genome alignment. These files can be used in genome browsers that allow the user to load several sequences simultaneously.

*strain*_super.gff  Contains the gene annotations of each strain mapped to the coordinate system of the SuperGenome.

*strain*_super*Type*Strand.gr Contains the xy-graphs of each strain mapped to the coordinate system of the SuperGenome. Type is either ‘FivePrime’ (treated) or ‘Normal’ (untreated). Strand is either ‘Plus’ or ‘Minus’. Note that the files now contain the value 0.0001 instead of 0 as a value of 0 (i.e. no entry line) now indicates a gap. This is necessary for IGB’s thresholding feature (see below).

superTSS.gff  Contains all TSS predicted in the four strains in the coordinate system of the SuperGenome. Also all TSS that were only predicted in one strain are listed. The information in how many strains (and in which) a TSS was detected is given in superClasses.tsv. In the header line all parameter names and values which are used for the run are reported.

TSSstatistics.tsv Contains some general statistics about the TSS prediction results.