From 9bb95bcc40f48e02ae2072668ae34581e0d65ffc Mon Sep 17 00:00:00 2001 From: Attayeb Date: Wed, 10 Jan 2018 11:07:51 +0900 Subject: [PATCH] update readme file --- README.md | 53 +++++++++++++++++++++++++++++------------------------ 1 file changed, 29 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index d968450..b284bc3 100755 --- a/README.md +++ b/README.md @@ -62,52 +62,57 @@ Auto-q determines R1 and R2 using the names of the files, please do not modify t ``` -usage: auto-q.py [-h] -i INPUT -o OUTPUT [-b BEGINWITH] [-t TRIM_THRESHOLD] - [-s STOP_AT] [-j JOINING_METHOD] [-p FASTQ_P] - [-q QC_THRESHOLD] [--continuation_reference C_REF] - [--continuation_otu_id C_OTU_ID] [-c CONFIGFILE] - [--adapter ADAPTER_REFERENCE] [-a MAPPING_FILE] +usage: auto-q.py [-h] -i Input folder -o Output folder + [-t trim_phred_threshold] [-p fastq-join p] + [--adapter ADAPTER_REFERENCE] [-b starting step] [-s stop at] + [-j joining method] [-m] [-q quality control threshold] + [--continuation_reference newref_seq.fna] + [--continuation_otu_id C_OTU_ID] [-r Reference database] + [-c Configuration file name] [-a Mapping file name] [--parameter_file_name PARAMETER_FILE_NAME] - [-n NUMBER_OF_CORES] [-f] [-m] [-r RDB] [-e DEPTH] - [--ml MINIMUM_LENGTH] + [-n Number of jobs] [-e Sampling depth] [--ml Minimum length] ``` ``` optional arguments: - optional arguments: -h, --help show this help message and exit - -i Input folder The folder where Fastq files are stored [required] - -o Output folder The folder of all results [required] - -t Phred threshold phred quality threshold for trimming [default: 12] - -p Percentage of mismatch - Percentage of mismatch fastq-join [default: 16] + -i Input folder the input sequences filepath (fastq files) [REQUIRED] + -o Output folder the output directory [REQUIRED] + -t trim_phred_threshold + phred quality threshold for trimming [default: 12] + -p fastq-join p fastq-join's percentage of mismatch [default: 16] --adapter ADAPTER_REFERENCE Adapters reference file - -b Step begin with: (otu_picking), (diversity_analysis) - -s Analysis step Terminate the analysis at this step - -j Joining method choose the merging method (fastq-join) or (bbmerge) + -b starting step starting the analysis in the middle: (otu_picking), + (diversity_analysis) + -s stop at terminate the analysis at this step [choices: + (merging), (quality_control), (chimera_removal)) + -j joining method choose the merging method (fastq-join) or (bbmerge) [default: fastq-join] -m Assign maxloose to be true for bbmerge [default: False] - -q Number quality control phred threshold [default: 19] + -q quality control threshold + quality control phred threshold [default: 19] --continuation_reference newref_seq.fna - Reference sequence for continuation + reference sequence for continuation. If you want to + continue analysis using the reference data set from + previous analysis. you can find it in the last sample + otus folder new_refseqs.fna --continuation_otu_id C_OTU_ID - continuation new reference set id + continuation reference new otus ids -r Reference database silva, greengenes [default: silva] -c Configuration file name Configuration file name [default: qiime.cfg] - -a MAPPING_FILE Mapping file name + -a Mapping file name Mapping file name --parameter_file_name PARAMETER_FILE_NAME The name of the parameter file [if not assigned is automatically produced using configuration file - -n Number of jobs Number of cores to be used for the analysis [default: - 2] - -e DEPTH set the depth of diversity analyses [default: 10000] - --ml MINIMUM_LENGTH Minimum length of reads kept after merging [default: + -n Number of jobs Specify the number of jobs to start with [default: 2] + -e Sampling depth sampling depth for diversity analyses [default: 10000] + --ml Minimum length Minimum length of reads kept after merging [default: 380] ```