Server

The data hub for the MfD project is the CMC server at the University of Aalborg, which is meant for internal collaborations.

Folder structure

The location of the MfD folder on the server is /projects/microflora_danica/ and the data/sequencing/ folder follows the following structure:

Folder	Content
├── raw/	Raw sequences
│   └── <sequence_type>/	Each folder will be self-descriptive about the the type of sequencing data included (shallow_metagenomes, ht_paper, etc)
│     └── files	Sequencing files named as <JOURNAL TYPE>-<JOURNAL NUMBER>-<WELL POSITION>_<SEQUENCING LANE>_<READ DIRECTION>.fastq.gz
├── trimmed/	Trimmed sequences
│   └── <sequence_type>/	Each folder will be self-descriptive about the the type of sequencing data included (shallow_metagenomes, ht_paper, etc)
│     └── files	Sequencing files named as <JOURNAL TYPE>-<JOURNAL NUMBER>-<WELL POSITION>_<SEQUENCING LANE>_<READ DIRECTION>.fastq.gz
└── gene_tables/	Tables of quantified genes

Where

• <JOURNAL TYPE> is an experimental batch, here always "LIB";
• <JOURNAL NUMBER> is in the form of two letters ("MJ") followed by three digits;
• <WELL POSITION> is the well position on the processing plate (a letter A-H and a number 1-12);
• <SEQUENCING LANE> is a two digits number for illumina sequences (01-04); and
• <READ DIRECTION> has the usual format "R1" and "R2".