Add documentation for NGS data with metadata #68
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jenniferboedker
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jenniferboedker
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Left some comments. Other then that LGTM
| **Disclaimer!** | ||
| This data format is targeted for a single use case and should not be | ||
| used for general data registration purposes. Please use the | ||
| [NGS single-end / paired-end data](#ngs-single-end--paired-end-data) | ||
| format for now. |
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Maybe point out what differentiates the two registration processes?
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Thats deep business, i actually would not like to have it here.
| ``` | ||
| { | ||
| "files": [ | ||
| "reads.1.fastq.gz", | ||
| "reads.2.fastq.gz" | ||
| ], | ||
| "type": "dna_seq", | ||
| "sample1": { | ||
| "genome": "GRCh37", | ||
| "id_genetics": "GS000000_01", | ||
| "id_qbic": "QTEST002AE", | ||
| "processing_system": "Test system", | ||
| "tumor": "no" | ||
| } | ||
| } | ||
| ``` |
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Nice, I like the example!
| <QBIC sample code> // Directory | ||
| |-- file1.fastq.gz | ||
| |-- file2.fastq.gz | ||
| |-- metadata |
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maybe make it more explicit
| |-- metadata | |
| |-- metadata.json |
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no, its metadata :) the script does not look for the json extension.
| Example sample ids: | ||
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| QABCD001AE (Analyte, Q_TEST_SAMPLE) | ||
| NGS[0-9]{2}QABCS001AE (Sequencing Result, Q_NGS_SINGLE_SAMPLE_RUN) where |
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Since we also give example for the codes I think its ok to also avoid the regex here
| NGS[0-9]{2}QABCS001AE (Sequencing Result, Q_NGS_SINGLE_SAMPLE_RUN) where | |
| NGS23QABCS001AE (Sequencing Result, Q_NGS_SINGLE_SAMPLE_RUN) where |
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I think it is important to now, how the code will look like. It will be always to digit, from 00-99.
| Q_TEST_SAMPLE -> Q_NGS_SINGLE_SAMPLE_RUN (with sample code) -> DataSet | ||
| of type Q_NGS_RAW_DATA (directory with raw sequencing files contained) |
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I cannot verify if this is the structure. I did not find an openbis project for that so I will trust you here :)
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