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README.md

File metadata and controls

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Directory structure

Throughout, we use the convention that your data directory has the following structure:

your/data/directory/
└── FASTQs/             # directory where your FASTQ files are
    ├── sample1_R1.fastq.gz
    ├── sample1_R2.fastq.gz
    ├── sample2_R1.fastq.gz
    ├── sample2_R2.fastq.gz
    └── ...
└── config.tsv          # tab-separated file containing metadata for your samples

config.tsv should contain all relevant metadata to your samples. Each row of config.tsv is a sample and each column is a particular feature you want to consider for pre-processing or analysis. A header row should be included.

config.tsv should contain at least a column titled Sample, that contains the sample name in the FASTQ file(s). For example:

Sample	Condition	SeqBatch
sample1	Control	A
sample2	Control	B
sample3	Treatment	B
sample4	Treamtent	C