From a36328d0e2980f58cfc36afa2640dfa2f00bb873 Mon Sep 17 00:00:00 2001
From: gailrosen <empr3ss@gmail.com>
Date: Mon, 12 Aug 2013 16:13:58 -0400
Subject: Update matlab.markdown
The other version was not properly viewable. Now it is.
---
doc/matlab.markdown | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
(limited to 'doc/matlab.markdown')
diff --git a/doc/matlab.markdown b/doc/matlab.markdown
index ec9249c..09b0103 100644
--- a/doc/matlab.markdown
+++ b/doc/matlab.markdown
@@ -120,15 +120,15 @@ their concentrations (in the first and second columns respectively)
Usage tips:
* Please name fasta files of sample reads with <sample id>.fa<*> and place them
- into one directory without any other f ile in that directory (for example, no
+ 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
- direct ory)
+ 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 <train ing_database_filename>
+* 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:
@@ -142,13 +142,17 @@ output:
Unweighted.)
Pre-requisites:
-1. <quikr_otu_table.txt>
+1. \<quikr\_otu\_table.txt\>
2. the tree of the database sequences that were used (e.g. dp7\_mafft.fasttree,
gg\_94\_otus\_4feb2011.tre, etc.)
-3. your-defined <qiime_metadata_file.txt>
+3. your-defined \<qiime\_metadata\_file.txt>
The QIIME procedue:
+
convert_biom.py -i <quikr_otu_table.txt> -o <quikr_otu>.biom --biom_table_type="otu table"
+
beta_diversity.py -i <quikr_otu>.biom -m weighted_unifrac -o beta_div -t <tree file> (example: rdp7_mafft.fasttree)>
+
principal_coordinates.py -i beta_div/weighted_unifrac_<quikr_otu>.txt -o <quikr_otu_project_name>_weighted.txt
+
make_3d_plots.py -i <quikr_otu_project_name>_weighted.txt -o <3d_pcoa_plotdirectory> -m <qiime_metadata_file>
--
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