Update analysis.rst

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EBI-Metagenomics · Jul 20, 2017 · 4067fdf · 4067fdf
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diff --git a/docs/analysis.rst b/docs/analysis.rst
@@ -70,6 +70,5 @@ Description of functional annotation files available to download
 
 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.
+- 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>`_.