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input_zip_structure.md

File metadata and controls

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For a zip file called ABC.zip, the structure in the file should include:

ABC/  # same as the zip filename
├── reads/  
│   ├── dna/  # paired-end DNA-seq reads
│   └── rna/  # single-end RNA-seq reads
├── functions/
│   └── functions  # a list of features to include; each one in a line 
├── reference/  # reference data
├── resources/
│   └── resources  # the resource allowance
└── phenotype/  # phenotype data

  • reads/dna/: This folder contains paired-end DNA-seq reads. Each file represents one end of reads of a sample. The files should be named after the sample names and have an extension of either .1.fastq.gz, .1.fq.gz, .2.fastq.gz, or .2.fq.gz, in which 1 and 2 represent the ends of read pairs.

  • reads/rna/: (optional) This folder contains single-end RNA-seq reads. Each file represents the reads of a sample. The files should be named after the sample names and have an extension of either .fastq.gz or .fq.gz.

  • reference/: This folder contains reference sequence and annotation files, of which the file extensions should be .fna (genome sequence; fasta format), .gbk (annotation genbank file), and gff (annotation gff file).

  • functions/functions: The file is adequate to the 'features' field of the yaml input file (see README.md). The file include the analyses to conduct. Each analyses are described in one row.

  • resources/resources: (optional) The file is adequate to the 'general -> cores' and 'general -> mem_mb' fields of the yaml input file (see README.md). This file should include two columns separated by tab, of which the first is the resource name (cores or mem_mb) and the second includes the values.

  • phenotype/: (optional) The phenotypes for differential expression analysis or model training (Geno2Pheno). The phenotype table should be formatted as described in the README.md and the filename should have an extension of .mat.