Changes between Version 1 and Version 2 of net.sf.basedb.reggie/notes423


Ignore:
Timestamp:
Aug 6, 2019, 12:05:47 PM (14 months ago)
Author:
Nicklas Nordborg
Comment:

Added instructions for creating barcode templates

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  • net.sf.basedb.reggie/notes423

    v1 v2  
    1818|| Raw bioassay || Cufflinks ||  -  || Legacy ||
    1919|| Raw bioassay || !StringTie ||  -  || TODO ||
    20 || Protocol || Demuxing ||  -  || RNAseq ||
    21 || Software || Demuxing ||  -  || RNAseq ||
     20|| Protocol || Demuxing, Merging ||  -  || RNAseq ||
     21|| Software || Demuxing, Merging ||  -  || RNAseq ||
    2222
    2323== 2. Other updates to existing items ==
     
    3131|| Protocol || Library preparation || !LibPrepTarget=MIPs || One or more protocols that will appear in the "MIPs library registration" wizard ||
    3232|| Protocol || Pooling || !LibPrepTarget=MIPs || One or more protocols that will appear in the MIPs pooling wizard ||
    33 || Protocol || Demuxing || Pipeline=MIPs || One or more protocols that will appear in the MIPs demux wizard ||
    34 || Software || Demuxing || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard ||
     33|| Protocol || Demuxing || Pipeline=MIPs || One or more protocols that will appear in the MIPs demux wizard (demux section) ||
     34|| Software || Demuxing || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard (demux section) ||
     35|| Protocol || Merging || Pipeline=MIPs || One or more protocols that will appear in the MIPs demux wizard (merge section) ||
     36|| Software || Merging || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard (merge section) ||
     37
     38== 4. Barcode templates ==
     39
     40Most of the barcode information (such as the sequences, positions, etc.) should be available as a file that can be used with batch importers. Some steps need to be done manually.
     41
     42 1. A barcode templates is represented as a **Bioplate** item where each coordinate is linked to a **Tag** item. Start by manually creating the required number of bioplates. They should have the following values:
     43
     44|| **Bioplate type** || !BarcodeTemplate ||
     45|| **Plate geometry** || 96-well (8x12) ||
     46|| **Pipeline** (annotation) || MIPs ||
    3547
    3648
     49 2. Import/create **Tag** items from file using the batch **Tag importer** and then add annotations with the **Annotation importer**. The following values are required:
     50
     51|| **Name** || Name of the barcode/tag which must be unique ||
     52|| **Pipeline** || All items should be set to `MIPs` ||
     53|| **!BarcodeSequence** || The barcode sequence for the first index read ||
     54|| **BarcodeSequence2** || The barcode sequence for the second index read ||
     55
     56 3.  Link the barcodes to templates. This is done by creating (virtual) extracts and link them with tags and positions on one of the bioplates created in the first step. It should be possible to do this with the batch **Extract importer**:
     57
     58|| **Name** || Name of the extract (recommended to be the same as the name of the Tag) ||
     59|| **Tag** || Name of the tag ||
     60|| **Bioplate** || Name of the template bioplate ||
     61|| **Biowell row** || Row coordinate on the template bioplate (A-H) ||
     62|| **Biowell column || Column coordinate on the template bioplate (1-12) ||