| 23 | | * Cohort data (in folder `cohortTables`): |
| 24 | | - TODO |
| | 23 | * Cohort data (in folder `cohortTables`): A set of tab-separated files with data for each raw bioassay and the parent items it is derived from. Each file starts with a header line. Each row contains data for one raw bioassay. The first column (`rba`) is always the name of the raw bioassay. |
| | 24 | - `cohortRawbioassay.txt`: Data from the raw bioassay level. Columns: |
| | 25 | * `ID`: Internal ID in BASE |
| | 26 | * `Name`: Name of raw bioassay |
| | 27 | * `Platform`: Name of platform (Sequencing) |
| | 28 | * `Raw.data.type`: Name of raw data type (cufflinks) |
| | 29 | * `Has.data`: Flag indicating if there is raw data for this raw bioassay or not (TRUE/FALSE) |
| | 30 | * `Db.spots`: Number of raw data entries |
| | 31 | * `Array.design`: Name of the array design |
| | 32 | * `Software`: Name of the software used to generate the raw data |
| | 33 | * `Import.date`: Date the raw data was created (in YYYY-MM-DD format) |
| | 34 | * `AnalysisResult..A.`: !Successful/Failed |
| | 35 | * `DataFilesFolder..A.`: Path to folder in project archive file server where data files are located |
| | 36 | * `FPKM.tracking.file..F.`: Path to the `isoforms.fpkm_tracking` file in the BASE file system |
| | 37 | - `cohortAligned`: Data from the `AlignedSequences` parent item. Columns: |
| | 38 | * TODO |
| | 39 | - `cohortMasked.txt`: Data from the `MaskedSequences` parent item. Columns: |
| | 40 | * TODO |
| | 41 | - `cohortMerged.txt`: Data from the `MergedSequences` parent item. Columns: |
| | 42 | * TODO |
| | 43 | - `cohortSequencing.txt`: Data from the `SequencingRun` parent item. Columns: |
| | 44 | * TODO |
| | 45 | - `cohortLibrary.txt`: Data from the `Library` parent item. Columns: |
| | 46 | * TODO |
| | 47 | - `cohortRNA.txt`: Data from the `RNA` parent item. Columns: |
| | 48 | * TODO |
| | 49 | - `cohortLysate.txt`: Data from the `Lysate` parent item. Columns: |
| | 50 | * TODO |
| | 51 | - `cohortSample.txt`: Data from the `Specimen` parent item. Columns: |
| | 52 | * TODO |
| | 53 | - `cohortCase.txt`: Data from the `Case` parent item (except INCA data). Columns: |
| | 54 | * TODO |
| | 55 | - `cohortPatient.txt`: Data from the `Patient` parent item. Columns: |
| | 56 | * TODO |
| | 57 | - `cohortStained.txt`: Data from the `Stained` parent item. Columns: |
| | 58 | * TODO |
| | 59 | - `cohortINCA.txt`: Data from parent items (eg. Case) that have been imported from the INCA registry. Columns: |
| | 60 | * TODO |
| | 61 | - `cohortSummaryTable.txt`: A single table collecting some of the most useful information from the other tables. |
| | 62 | |
| | 63 | * Subtype data (in folder `cohortTables/subtypeTables`): Information generated by the R report scripts. We do not currently store this information in BASE, so it needs to be discussed how this should be done. The report plug-in could for example import the data from the R scripts as annotations. |
