Update analysis.rst

added taxonomy file description

docs/analysis.rst

@@ -62,3 +62,14 @@ Description of fasta files available to download
 - Reads encoding 16S rRNA: this file contains all reads predicted to encode for 16S rRNA by rRNASelector.
 - Reads encoding 23S rRNA: this file contains all reads predicted to encode for 23S rRNA by rRNASelector.
 
+Description of functional annotation files available to download
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+- InterPro matches file:  it is a tab-delimited file containing 15 columns. They are fully described `here <https://github.com/ebi-pf-team/interproscan/wiki/OutputFormats>`_
+- Complete GO annotation file: it is a comma-separated file containing 4 colums. The first column lists the GO terms (labelled GO:XXXXXXX) having been associated to the predicted CDSs. The second gives the GO term description while the third indicates which category the GO term belong to. There is 3 category: ‘biological process’ (higher biological process such as ‘rRNA modification’) , ‘molecular function’ (individual catalytic activity such as ‘mannosyltransferase activity’) and ‘cellular component’ (cellular localisation of the activty such as ‘mitochondrion’). The last column give the number of predicted CDSs having been annotated with the GO terms for the run.
+- GO slim annotation file: this file is derived from the 'Complete GO annotation file' and has the same format. The GO slim set is a cut-down version of the GO terms containing a subset of the terms in the whole GO. They give a broad overview of the ontology content without the details of the specific fine grained terms. Go slim terms are used for visualisation on the website. To illustrate how the GO slim terms relates to the GO terms, the different metal binding GO terms present in the ‘Complete GO annotation’ file are summarized as one generic metal binding term in the ‘GO slim annotation’ file. The last column give the number of predicted CDSs having been annotated with the GO slim terms for the run.
+
+Description of taxonomic assignment files available to download
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+- OTUs, reads and taxonomic assignments files: the 3 file available to download contain the same data in 3 differnt format : tab-separated file (TSV) and two Biom file (HD5F and JSON). The TSV file contains 3 columns which headers are in the second line of the file. The first column is the OTU Id. These can be compared between runs as they have been generated using `Qiime closed-reference protocol <http://qiime.org/tutorials/otu_picking.html>`_ for version 2 and 3 of the pipeline. The second column indicates the number of predicted 16S sequences associated with each OTU. The third column contains the taxonomic lineages provided by `GreenGenes database (http://greengenes.lbl.gov/cgi-bin/nph-index.cgi>`_. Note that the number of unannotated 16S sequences is not indicated in this file. This file can be directly imported into `Megan6 <http://ab.inf.uni-tuebingen.de/software/megan6/>`_ for visualisation and further analysis.
+The Biom files are `computer-readable files <http://biom-format.org>`_. The HD5F (Hierachical Data Format) format can be imported into analysis and visualisation tools such as Matlab and R. A larger number of commercial and freely available tools, such as MEGAN6, can consume the JavaScript Object Notation (JSON) format.
+- Phylogenetic tree (Newick format)’ file (only available up to version 3 of EBI Metagenomics pipeline): this file can be used to visualise the hierarchical distribution of the taxonomic lineages of each run. The `Newick format <https://en.wikipedia.org/wiki/Newick_format>`_ is a computer-readable format to represent the tree and can be directly imported into freely-available viewers such as `FigTree <http://tree.bio.ed.ac.uk/software/figtree>`_ and `ITOL (interactive Tree of Life, <http://itol.embl.de>`_.