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Database info

This tab shows some information about the database content. Additionally it is possible to export most of this content into files. To do this, use the 'Export'-buttons on the left side of the tab.

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The right half of the tab contains the list of the different sequencing runs included in the database. Every cell in the table can be edited, the modifications will be saved by pressing the 'Save changes'-button. The first 3 columns of the table are the most important ones, because they have a direct effect to other functions such as 'Database statistics' or 'Mapping'. With the first column, the runs are selected, that shall be used by other functions. The second column sets the color in which the reads of the accordant run are displayed. The third column shows, if a run is treated as 'control' or 'stress', this is important for comparing two groups of runs (Expression analysis).
With the 'Add Run'-button the read sequences of a new sequencing run can be added to the database.
The 'Coverage'-button calculates how much of the sequence information in the database covered by the selected runs.

Add run

The 'Add run'-option writes the sequences from a fasta file as reads into the database, if a file is given. Only the 'ID' has to be set, otherwise the run cannot be added. The other field could be left empty, they can be edited any time.

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Coverage

The 'Coverage'-option calculates the number of bases, of the whole transcriptome, covered by the reads of the selected runs and counts all contigs, that are partially covered those reads. The results are not correct to the last base, because of insertions and deletions in the reads.

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'Export'-buttons

Export sequences
With the first three export buttons the contig, protein and read sequences can be exported to a fasta file. While exporting the contig sequences it is possible to select a subset of contigs, which have blast annotations or annotations of a specific domain database (pfam, smart, ..). If such a subset is chosen the description of the best annotation hit of the selected category can be attached to the fasta header of each sequence.
While exporting read sequences it is possible to choose to export just the singleton reads, the assembled reads, the reads of a specific run or all reads.

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Export features
With the fourth export button a list of all different hits, including their descriptions, will be exported to a tab-delimited text file, for each selected feature. If the option 'with contigs' is selected each hit entry also lists it associated contigs.

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