Changes between Version 4 and Version 5 of userguide

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Timestamp:
06-10-11 16:19:00 (3 years ago)
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r.w.w.brouwer@…
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  • userguide

    v4 v5  
    33== Samplesheet == 
    44 
    5 NARWHAL will obtain sample information from a tab-delimited sample-sheet. The sample-sheet is a tab-delimited format with a fixed column order. Withing the columns, values can be delimited up to 2 levels deep using commas and semicoloms repectively. The format of the sample-sheet is as follows: 
     5NARWHAL will obtain sample information from a tab-delimited sample-sheet. The sample-sheet is a tab-delimited format with a fixed column order. Withing the columns, values can be delimited up to 2 levels deep using commas and semicolons repectively. The format of the sample-sheet is as follows: 
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     8||Column||Description||Comment|| 
     9||1||Sample ID|| This value should not contain spaces. The LaTEX document processor used to create the PDF QC report is not able to process samples with spaces|| 
     10||2||Lane number||The lane number in which the sample is present.|| 
     11||3||Data reads*||If multiple data reads are present these should be comma delimited.|| 
     12||4||multiplex sequence (barcode)*||The barcode sequence.|| 
     13||5||multiplex start sites*||In NARWHAL, barcodes are not required to start at the first base. In this field, the 0-offset barcode start should be present.|| 
     14||7||Index read*||The read that contains the barcode sequence.|| 
     15||8||Reference sequence||The path to the reference sequence.|| 
     16||9||Paired end alignment||Should a paired-end alignment be performed?|| 
     17||10||Application profile||The alignment settings and tool that will be used to align the data files for this sample are specified by the application profile. The application profiles are specified in the json configuration file.|| 
     18||11||Additional options||Additional options can be specified in this field. The options should be comma delimited in a specific option format. This option format should be [sub-tool]:key=value. Key and value are mandatory and the sub-tool is optional. For an example see example 1.|| 
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    820== Quick start ==