From d4775d263a02fa5ec673a0043d741385f5f42320 Mon Sep 17 00:00:00 2001 From: Markus Ankenbrand Date: Tue, 4 Aug 2015 11:22:33 +0200 Subject: [PATCH] added Quick Start section that describes how to classify own data --- README.org | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/README.org b/README.org index 97695e9..976556d 100644 --- a/README.org +++ b/README.org @@ -28,6 +28,37 @@ Only the RDP training was performed on a machine with more RAM available. - [[http://qiime.org/][QIIME]] (Version 1.8.0+dfsg-4) - [[https://code.google.com/p/ea-utils/wiki/FastqJoin][fastq-join]] (Version 1.01.759) +* Quick Start +If you want to start to classify your own data right now, this is the easiest way to do it: + - Make sure you have installed perl, usearch, fastq-join (and RDPclassifier if needed). + - Put all your fastq read files in an empty directory + - Execute the following commands: +#+BEGIN_SRC sh +# git clone the repository +git clone https://github.com/iimog/meta-barcoding-dual-indexing +# alternatively you can download and extract the release + +cd meta-barcoding-dual-indexing +mkdir myanalyses +cd myanalyses +# extract the plant reference databases for classification +tar xzvf ../training/rdp/rdp_trained.tar.gz +tar xzvf ../training/utax/utax_trained.tar.gz + +# this step is not required but recommended +# if you choose to skip it use .fa instead of .udb when calling classify_reads.pl +usearch -makeudb_usearch utax_trained/viridiplantae_all_2014.utax.fa\ + -output utax_trained/viridiplantae_all_2014.utax.udb + +# call the wrapper script that performs: +# joining, filtering, classification and aggregation for all samples +perl ../code/classify_reads.pl --out results /*.fastq\ + --utax-db utax_trained/viridiplantae_all_2014.utax.udb\ + --utax-taxtree utax_trained/viridiplantae_all_2014.utax.tax\ + --rdp --rdp-jar /classifier.jar\ + --rdp-train-propfile rdp_trained/its2.properties + +#+END_SRC * Workflow ** Preparation of Reference Database *** Data