From dd20b8e4efb4a6c5090d76459f3fdb0885367477 Mon Sep 17 00:00:00 2001 From: Calvin Date: Fri, 3 May 2013 16:56:11 -0400 Subject: updated documentation , added multi_gg_final.m --- src/matlab/multifasta2otu/README | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 src/matlab/multifasta2otu/README (limited to 'src/matlab/multifasta2otu/README') diff --git a/src/matlab/multifasta2otu/README b/src/matlab/multifasta2otu/README new file mode 100644 index 0000000..40031e6 --- /dev/null +++ b/src/matlab/multifasta2otu/README @@ -0,0 +1,22 @@ +* Please name fasta files of sample reads with .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 , , , and + +To use with QIIME, one must run the QIIME conversion tool on our OTU table output: +convert_biom.py -i -o .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) , 2) the tree of the database sequences that were used (e.g. +rdp7_mafft.fasttree, gg_94_otus_4feb2011.tre, etc.), and 3) your-defined + +1. convert_biom.py -i -o .biom --biom_table_type="otu table" +2. beta_diversity.py -i .biom -m weighted_unifrac -o beta_div -t +3. principal_coordinates.py -i beta_div/weighted_unifrac_.txt -o _weighted.txt +4. make_3d_plots.py -i _weighted.txt -o <3d_pcoa_plotdirectory> -m + -- cgit v1.2.3