From 30b44dd4c53b01fa0ff5b122929376c76495c351 Mon Sep 17 00:00:00 2001 From: idfarbanecha Date: Mon, 12 Jul 2021 12:00:07 +0200 Subject: [PATCH] updated README --- README.md | 37 +++++++++++++++++-------------------- input_table.tsv | 2 +- 2 files changed, 18 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 14d957e..a37bd7d 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ relative abundances. #### Read percentage Below is an example of input table where the user can set, for each entry, read percentages of the total metagenomic reads -UserInputNames | nb_genomes | PercentReads +TaxonomyInput | nb_genomes | PercentReads --- | --- | --- 1813735 | 1 | 0.3 114185 | 1 | 0.4 @@ -32,7 +32,7 @@ In the input table shown above, if no PercentReads is present, each entry will h #### Coverage values The user has also the option to set coverage values instead of %reads of the total metagenomic reads for each entry. -UserInputNames | nb_genomes | Coverage +TaxonomyInput | nb_genomes | Coverage --- | --- | --- 1813735 | 1 | 20 114185 | 1 | 30 @@ -43,7 +43,7 @@ In this case, all 3 assemblies found for ATCC_13985 will have the same coverage Alternatively, the user can specify relative proportions between assemblies. Given the total number of reads to be present in the metagenome, scripts will calculate coverage and read numbers respecting the relative proportions. -UserInputNames | nb_genomes | RelativeProp +TaxonomyInput | nb_genomes | RelativeProp --- | --- | --- 1813735 | 1 | 0.3 114185 | 1 | 0.4 @@ -54,7 +54,7 @@ For ATCC_13985, the 3 genomes will have a RelativeProp value of 0.1. ```yaml #MeSS parameters input_table_path: input_table.tsv -community_name: metagenome-1 +community_name: metagenome-sim #Replicates parameters replicates: 1 sd_read_num: 0 @@ -152,16 +152,15 @@ mess run -c 10 Runs the Mess workflow using 10 cores. ## MeSS outputs ### Directory structure -After running MeSS, your working directory should look like this: +After running MeSS for two replicates of the same metagenome with single end reads, +your working directory should look like this: ``` ├── assembly_gz │ ├── assembly-accession-1.fna.gz │ └── assembly-accession-2.fna.gz ├── krona -│ ├── sample-1-metagenome -│ │ └── replicate-1-krona-plot.html -│ └── sample-2-metagenome -│ └── replicate-1-krona-plot.html +│ ├── metagenome-sim-rep1_single.html +│ └── metagenome-sim-rep2_single.html ├── logs │ ├── downloads │ ├── filtered @@ -170,21 +169,19 @@ After running MeSS, your working directory should look like this: │ ├── read_generation │ └── shuffling ├── simreads -│ ├── sample-1-metagenome -│ │ └── replicate-1 -│ │ └── simulated-reads.fastq -│ ├── sample-2-metagenome -│ │ └── replicate-1 -│ │ └── simulated-reads.fastq +│ ├── metagenome-sim-rep1_single.fastq +│ ├── metagenome-sim-rep1_single.fastq ├── tables │ ├── filtered │ └── not-filtered ├── config.yaml ├── input_table.tsv -├── summary-metagenome-1.tsv -├── summary-metagenome-2.tsv -└── assemblies-summary.tsv +├── readcounts-metagenome-sim-rep1.tsv +├── readcounts-metagenome-sim-rep2.tsv +├── metagenome-sim-assemblies-summary.tsv +├── taxonomy-metagenome-sim-rep1_single.tsv +└──taxonomy-metagenome-sim-rep2_single.tsv ``` -The simulated reads fastqs are compressed and located in the simreads/ directory, and their composition is summarized in -summary-.tsv. +The simulated reads fastqs are compressed and located in the simreads/ directory, and their taxonomic profile is in +taxonomy---.tsv. diff --git a/input_table.tsv b/input_table.tsv index 18b8438..cb2e2ea 100644 --- a/input_table.tsv +++ b/input_table.tsv @@ -1,3 +1,3 @@ -UserInputNames nb_genomes +TaxonomyInput nb_genomes 1813735 1 114185 1