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Diffstat (limited to 'src/matlab/README_for_multifasta2otu')
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diff --git a/src/matlab/README_for_multifasta2otu b/src/matlab/README_for_multifasta2otu new file mode 100644 index 0000000..05a26c6 --- /dev/null +++ b/src/matlab/README_for_multifasta2otu @@ -0,0 +1,27 @@ +* Quikr multifasta->otu_table_(for_qiime_use) wrapper code written by Gail Rosen -- 2/1/2013 + +Usage tips: +* Please name fasta files of sample reads with <sample id>.fa<*> and place them into one directory without any other file in that directory (for example, no hidden files that the operating system may generate, are allowed in that directory) +* Note: When making your QIIME Metadata file, the sample id's must match the fasta file prefix names +* Fasta files of reads must have a suffix that starts with .fa (e.g.: .fasta and .fa are valid while .fna is NOT) +* Modify the top of the Matlab/Octave scripts for <input_directory>, <output_directory>, <output_filename>, and <training_database_filename> + +To use with QIIME, one must run the QIIME conversion tool on our OTU table output: +convert_biom.py -i <quikr_otu_table.txt> -o <quikr_otu>.biom --biom_table_type="otu table" + +--------------------------- + +4-step QIIME procedure after using Quikr to obtain 3D PCoA graphs: +(Note: Our code works much better with WEIGHTED Unifrac as opposed to +Unweighted.) + +Pre-requisites: +1. <quikr_otu_table.txt> +2. the tree of the database sequences that were used (e.g. rdp7_mafft.fasttree, gg_94_otus_4feb2011.tre. they are in the data directory) +3. your-defined <qiime_metadata_file.txt> + +1. convert_biom.py -i <quikr_otu_table.txt> -o <quikr_otu>.biom --biom_table_type="otu table" +2. beta_diversity.py -i <quikr_otu>.biom -m weighted_unifrac -o beta_div -t <tree file (example: rdp7_mafft.fasttree)> +3. principal_coordinates.py -i beta_div/weighted_unifrac_<quikr_otu>.txt -o <quikr_otu_project_name>_weighted.txt +4. make_3d_plots.py -i <quikr_otu_project_name>_weighted.txt -o <3d_pcoa_plotdirectory> -m <qiime_metadata_file> + |