diff options
Diffstat (limited to 'doc/cli.markdown')
| -rw-r--r-- | doc/cli.markdown | 12 |
1 files changed, 6 insertions, 6 deletions
diff --git a/doc/cli.markdown b/doc/cli.markdown index e12f6a9..fa7bab3 100644 --- a/doc/cli.markdown +++ b/doc/cli.markdown @@ -47,7 +47,6 @@ quikr returns the solution vector as a csv file. -o, --output OTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output) -v, --verbose verbose mode. -V, --version print version. - -d, --debug debug mode, read manpage for more details ## Multifasta\_to\_otu ## The Multifasta\_to\_otu tool is a handy wrapper for quikr which lets the user @@ -58,7 +57,7 @@ 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 +66,7 @@ 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 +91,11 @@ 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 +105,7 @@ 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. |