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| author | Calvin Morrison <mutantturkey@gmail.com> | 2013-08-30 13:25:46 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2013-08-30 13:25:46 -0400 |
| commit | 052ac4f46057030e8c489bba29458ee56437cdef (patch) | |
| tree | 74b24a13d357d7c7b4418d32c60835e9a105ed39 /doc/cli.markdown | |
| parent | 50824f178a11861124407840e8b226acf325f86a (diff) | |
Update cli.markdown
Fix markdown formatting, and add some details about the pre-requisites for multifasta
Diffstat (limited to 'doc/cli.markdown')
| -rw-r--r-- | doc/cli.markdown | 11 |
1 files changed, 6 insertions, 5 deletions
diff --git a/doc/cli.markdown b/doc/cli.markdown index e12f6a9..42af4b6 100644 --- a/doc/cli.markdown +++ b/doc/cli.markdown @@ -58,7 +58,7 @@ Warning: 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 python with run one job per cpu core. -# Pre-processing of Multifasta\_to\_otu # +### Pre-processing of Multifasta\_to\_otu ### * 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 @@ -67,7 +67,7 @@ with aspecified number of jobs. Otherwise python with run one job per cpu core. * Fasta files of reads must have a suffix that starts with .fa (e.g.: .fasta and .fa are valid while .fna is NOT) -### Usage ### +#### Usage #### multifasta_to_otu's arguments: -i, --input-directory the directory containing the samples' fasta files of @@ -92,10 +92,11 @@ with aspecified number of jobs. Otherwise python with run one job per cpu core. Unweighted.) Pre-requisites: -1. <quikr_otu_table.txt> + +1. quikr_otu_table.txt (The OTU Table generated with multifasta_to_otu 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 ( a Qiime Map file) The QIIME procedue: @@ -105,7 +106,7 @@ The QIIME procedue: make_3d_plots.py -i <quikr_otu_project_name>_weighted.txt -o <3d_pcoa_plotdirectory> -m <qiime_metadata_file> -#### Broken Pipe Errors #### +## Broken Pipe Errors ## Make sure that you have the count-kmers and probablilties-by-read in your $PATH, and that they are executable. |