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diff --git a/src/c/multifasta_to_otu.1 b/src/c/multifasta_to_otu.1 new file mode 100644 index 0000000..7878ef0 --- /dev/null +++ b/src/c/multifasta_to_otu.1 @@ -0,0 +1,95 @@ +.TH multifasta_to_otu 1 multifasta_to_otu-2013-05 +.SH NAME +multifasta_to_otu \- create a QIIME OTU table based on Quikr results. +.SH SYNOPSIS +.B multifasta_to_otu +.RB [ \-i +.IR input-directory ] +.RB [ \-f +.IR sensing-fasta] +.RB [ \-s +.IR sensing-matrix] +.RB [ \-k +.IR kmer ] +.RB [ \-l +.IR lambda ] +.RB [ \-j +.IR jobs ] +.RB [ \-o +.IR otu-table] +.RB [ \-v ] +.P +.BR multifasta_to_otu " ..." +.SH DESCRIPTION +.B multifasta_to_otu +The multifasta_to_otu tool is a handy wrapper for quikr which lets the user +to input as many fasta files as they like, and then returns an OTU table of the +number of times a specimen was seen in all of the samples. +.P +.SH OPTIONS +.TP +.B \-i, --input-directory +the directory containing the samples' fasta files of reads (note each fasta file should correspond to a separate sample) +.TP +.B \-f, --sensing-fasta +location of the fasta file database used to create the sensing matrix. +.TP +.B \-s, --sensing-matrix +location of the sensing matrix. +.TP +.b \-k, --kmer +specify what size of kmer to use. (default value is 6) +.TP +.B \-l, --lambda +lambda value to use. (default value is 10000) +.TP +.B \-j, --jobs +specifies how many jobs to run at once. (default value is the number of CPUs) +.TP +.B \-o, --otu-table +the OTU table, with OTU_FRACTION_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or sequence table if not OTU's) +.TP +.B \-v, --verbose +verbose mode. +.SH USAGE +This program will use a large amount of memory, and CPU time. +You can reduce the number of cores used, and thus memory, by specifying the -j flag with aspecified number of jobs. Otherwise multifasta_to_otu will run one job per cpu core. +.SH POSTPROCESSING +.B Note: When making your QIIME Metadata file, the sample id's must match the sample fasta file prefix names +.P +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.) +.TP +Pre-requisites: +1. multifasta output file "quikr_output_table.txt" for our example. +.br +2. the tree of the database sequences that were used (e.g.dp7_mafft.fasttree, gg_94_otus_4feb2011.tre, etc.) +.br +3. your-defined <qiime_metadata_file.txt> +.TP +The QIIME procedue: +convert_biom.py -i <quikr_otu_table.txt> -o <quikr_otu>.biom --biom_table_type="otu table" +.br +beta_diversity.py -i <quikr_otu>.biom -m weighted_unifrac -o beta_div -t <tree file> +.br +principal_coordinates.py -i beta_div/weighted_unifrac_<quikr_otu>.txt -o <quikr_otu_project_name>_weighted.txt +.br +make_3d_plots.py -i <quikr_otu_project_name>_weighted.txt -o <3d_pcoa_plotdirectory> -m <qiime_metadata_file> +.SH "SEE ALSO" +\fBquikr\fP(1), \fBquikr_train\fP(1). +.SH AUTHORS +.B multifasta2otu +was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison +<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, Jean-Luc Bouchot +.SH REPORTING BUGS +.TP +Please report all bugs to Gail Rosen <gailr@ece.drexel.edu>. Include your \ +operating system, current compiler, and test files to reproduce your issue. +.SH COPYRIGHT. +Copyright \(co 2013 by Calvin Morrison and Gail Rosen. Permission to use, +copy, modify, distribute, and sell this software and its documentation for +any purpose is hereby granted without fee, provided that the above copyright +notice appear in all copies and that both that copyright notice and this +permission noticeappear in supporting documentation. No representations are +made about the suitability of this software for any purpose. It is provided +"as is" without express or implied warranty. + |