INTRODUCTION
This directory is part of the official repository of public bioinformatics
data sets available from IFREMER research teams.

PROJECT livacid
RNAseq analysis reveals that transgenerational exposure to ocean acidification impacts the hepatic transcriptome of European sea bass (Dicentrarchus labrax).

PUBLICATION
Published to ENA under the accession number PRJEB59362.
See: https://www.ebi.ac.uk/ena/browser/view/PRJEB59362

DOI: https://doi.org/10.12770/5b94a252-13df-421e-ac39-1301912f90e2

DATA ORGANIZATION
Project is organized as follows: data is distributed
within several sub-folders all of them being named using the
EDAM Ontology (https://www.ebi.ac.uk/ols/ontologies/edam).
 
1/ Raw data is available from the 'data' sub-folder.

2/ Results from processing raw data is available in 'operation' sub-folder.

3/ In turn, sub-folders within 'data' and 'operation' rely on EDAM terms
depending on data type (data sub-folder) or operation type (operation
sub-folder).

DIRECTORY CONTENT
Raw fastq files are located in data/rna-sequence-raw folder.
Metadata are located in data/report/athena where one can find 2022_RNA-Seq_LIVACID.xlsx Excel file.
Metadata are also accessible through data/report/athena/XML XML files.

DATA RETRIEVAL
wget -r -np -nH --cut-dirs=4 ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/pfom/livacid

Command-line explained:

          -r: is for recursively download;
         -np: is for no parent ascending;
         -nH: is for disabling creation of directory having name same as URL i.e. ftp.ifremer.fr;
  --cut-dirs: is for ignoring number of parent directories.
see https://data-dataref.ifremer.fr/bioinfo/ifremer/README.txt for more details.