The 'Database statistics'-tab allows different kinds of overviews of the selected database through the 'Coverage' and 'Frequency' options. The 'Expression analysis'-option calculates the fraction of stress and control reads in each contig, depending on the run settings in the 'Database info'-tab.
The '<' (previous) and '>' (next) buttons enable switching between already created 'Database statistics'-lists, with the 'Remove'-button the currently opened list can be deleted.
The tab shows normally a diagram, but it can be switched to a tab-delimited list of the results by selecting the 'List'-radiobutton instead of the 'Diagram'-radiobutton.
Contig coverage
This shows the average coverage for each contig within the given parameters. The diagram shows a dot for each contig, its position depends on the contig length (x-axis) and the contigs average coverage (y-axis).
Coverage num. of reads
This diagram also shows a dot for each contig, but here its position depends on the contig length (x-axis) and the number of reads contained in the contig (y-axis).
Coverage per base
This function calculates the coverage for each base in each contig in the database. Then it counts, for each different coverage value, the number of bases, which have the same coverage value. The diagram shows bars for each coverage value. The height of a bar depends on the number of bases, which have the coverage that is associated with the bar. The number of bases (y-axis) is displayed in logarithmic values, the maximal displayed value is 100.000. To see absolute values switch to the list.
Coverage per base (gaps)
This is the same as 'Coverage per base', with the difference, that also the coverage of the gaps in the contigs is counted.
'Expression analysis' tries to calculate the number of A and B reads in a contig. For this the run table in the 'Database info'-tab is very important. Only reads from runs that are selected in the run table are used for this calculation. Also it is important, that some of the selected runs are marked as A and others as B.
The different options use the following functions for the calculation:
c: control reads; s: stress reads
Linear
x-axis: c; y-axis: s
Log2
x-axis: log2(c); y-axis: log2(s)
Fold change
if B > A:
y-axis: B/A
if B < A:
y-axis: -A/B
Fold change (Log2)
if B > A:
y-axis: log2(B/A)
if B < A:
y-axis: log2(-A/B)
Under 'Fold change' the down- and/or up-regulated contigs can be send into project tabs. To do this, just press the 'Show UP'- and/or 'Show DOWN'-button.
The list view shows a table of all contigs which match the parameter settings. The list can be exported through a right-click menu. The menu also allows to hide or unhide most of the available columns of the list.
When changing parameters it is not necessary to run the calculation again, it suffices to press the 'Refresh'-button. Only after a change in the given dataset or the 'Min. number of reads'-option the calculation has to run again.
Contigs by length
It shows the number of contigs within a certain length range, the range is defined by the 'Step width'-parameter. The diagram shows bars for each contig length range. The height of a bar depends on the number of contigs, which have a length in the range that is associated with the bar. The number of contigs (y-axis) is displayed in logarithmic values. To see absolute values switch to the list.
Reads by length
This is the same as 'Contigs by length', but instead of the contig lengths it displays the read length distribution.
Contigs by reads
This function counts the number of contigs, which consist of the same number of reads. The diagram shows bars for each read number range, the range is defined by the 'Step width'-parameter. The number of contigs (y-axis) is displayed in logarithmic values. To see absolute values switch to the list.