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| -rw-r--r-- | doc/cli.markdown | 55 |
1 files changed, 29 insertions, 26 deletions
diff --git a/doc/cli.markdown b/doc/cli.markdown index 3d7a636..587d014 100644 --- a/doc/cli.markdown +++ b/doc/cli.markdown @@ -12,11 +12,11 @@ Before running the quikr utility, you need to generate the sensing matrix. quikr\_train returns a custom sensing matrix that can be used with the quikr function. -quikr\_train's arguments: - -i, --input, the database of sequences (fasta format) - -o, --output, the sensing matrix (text file) - -k, --kmer, specifiy wha size of kmer to use. (default value is 6) - -v, --verbose, verbose mode. + quikr_train's arguments: + -i, --input, the database of sequences (fasta format) + -o, --output, the sensing matrix (text file) + -k, --kmer, specifiy wha size of kmer to use. (default value is 6) + -v, --verbose, verbose mode. ### Example ### Here is an example on how to train a database. This uses the -z flag to compress @@ -34,13 +34,13 @@ input FASTA file. You need to train a matrix or download a new matrix ### Usage ### quikr returns the solution vector as a csv file. -quikr's arguments: - -f, --fasta, the sample's fasta file of NGS READS - -o, --output OTU\_FRACTION\_PRESENT, a vector representing the percentage of - database sequence's presence in sample (csv output) - -s, --sensing-matrix the sensing matrix. (generated by quikr\_train) - -l, --lambda, the lambda size. (the default lambda value is 10,000) - -k, --kmer, this specifies the size of the kmer to use (default is 6) + quikr's arguments: + -f, --fasta, the sample's fasta file of NGS READS + -o, --output OTU\_FRACTION\_PRESENT, a vector representing the percentage of + database sequence's presence in sample (csv output) + -s, --sensing-matrix the sensing matrix. (generated by quikr\_train) + -l, --lambda, the lambda size. (the default lambda value is 10,000) + -k, --kmer, this specifies the size of the kmer to use (default is 6) ## Multifasta\_to\_otu ## The Multifasta\_to\_otu tool is a handy wrapper for quikr which lets the user @@ -61,19 +61,20 @@ with aspecified number of jobs. Otherwise python with run one job per cpu core. .fa are valid while .fna is NOT) ### Usage ### -multifasta\_to\_otu's arguments: - -i, --input, the directory containing the samples' fasta files of - reads (note each fasta file should correspond to a separate sample) - -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) - -s, --sensing-matrix, the sensing matrix - -f, --sensing-fasta, the fasta file database of sequences - -l, --lambda, specify what size of lambda to use (the default value is 10,000) - -k, --kmer, specify what size of kmer to use, (default value is 6) - -j, --jobs, specifies how many jobs to run at once, (default=number of CPUs) - -# Post-processing of Multifasta\_to\_otu # + + multifasta\_to\_otu's arguments: + -i, --input, the directory containing the samples' fasta files of + reads (note each fasta file should correspond to a separate sample) + -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) + -s, --sensing-matrix, the sensing matrix + -f, --sensing-fasta, the fasta file database of sequences + -l, --lambda, specify what size of lambda to use (the default value is 10,000) + -k, --kmer, specify what size of kmer to use, (default value is 6) + -j, --jobs, specifies how many jobs to run at once, (default=number of CPUs) + +### Post-processing of Multifasta\_to\_otu ### * Note: When making your QIIME Metadata file, the sample id's must match the sample fasta file prefix names @@ -89,12 +90,14 @@ Pre-requisites: 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> -#### 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. |