... | ... | @@ -26,6 +26,147 @@ A fully documented use case is available [HERE](https://umrf.pages.mia.inra.fr/r |
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Datasets to reproduce the use case are available at this [link](https://nextcloud.inrae.fr/s/Zx3iASe64x8oSoM)
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## DADA2 usage according to raw data type
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### IonTorrent single end
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* Trim primers with CUTADAPT
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```r
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dada_res = dada2_fun(cutadapt = TRUE, f_primer = "GTGYCAGCMGCCGCGGTAA", r_primer = "CCGYCAATTYMTTTRAGTTT",
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orient_torrent = "GTG",
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path = "./reads/sapoval_reads_links/", outpath = "./analyses/01_results_dada2/",
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torrent_single = TRUE, paired = FALSE)
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```
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* Trim primers based on length
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```r
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dada_res = dada2_fun(cutadapt = FALSE, trim_l = 20, trim_r = 21,
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orient_torrent = "GTG",
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path = "./reads/sapoval_reads_links/", outpath = "./analyses/01_results_dada2/",
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torrent_single = TRUE, paired = FALSE)
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```
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### Illumina paired end
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* Trim primers with CUTADAPT
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```r
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dada_res = dada2_fun(cutadapt = TRUE, f_primer = "CCTACGGGNGGCWGCAG", r_primer = "GACTACHVGGGTATCTAATCC",
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path = "./reads/", outpath = "./analyses/01_results_dada2/",
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torrent_single = FALSE, paired = TRUE,
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extension = "_R1.fastq.gz")
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```
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* Trim primers based on length
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```r
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dada_res = dada2_fun(cutadapt = FALSE, trim_l = 18, trim_r = 22,
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path = "./data/dataset_5k_illumina_paired", outpath = "./analyses/illumina_paired/01_results_dada2/",
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compress = TRUE, torrent_single = FALSE, paired = TRUE,
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extension = "_R1.fastq.gz")
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```
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### Illumina single end
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* Trim primers with CUTADAPT
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```r
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dada_res = dada2_fun(cutadapt = TRUE, f_primer = "CCTACGGGNGGCWGCAG", r_primer = "GACTACHVGGGTATCTAATCC",
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path = "./reads/", outpath = "./analyses/01_results_dada2/",
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torrent_single = FALSE, paired = FALSE)
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```
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* Trim primers based on length
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```r
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dada_res = dada2_fun(cutadapt = FALSE, trim_l = 18, trim_r = 22,
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path = "./data/dataset_5k_illumina_single", outpath = "./analyses/01_results_dada2/", compress = TRUE,
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torrent_single = FALSE, paired = FALSE)
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```
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## Databases
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We share all the databases we currently use for IDTAXA in this [link](https://nextcloud.inrae.fr/s/Zx3iASe64x8oSoM).
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## List of functions
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### Preprocessing
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`ranomaly::dada2_fun` : Processing of raw data from IonTorrent/Illumina tech. single/paired end, for raw ASV table generation.
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`ranomaly::generate_tree_fun` : Generate phylogenetic tree based on ASV representative sequences.
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`ranomaly::idTaxa_assign` : Taxonomy assignement with IDTAXA.
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`ranomaly::assign_taxo_fun` : Assign representative sequences from dada2_fun output.
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`ranomaly::idtaxa_assign_fasta_fun` : Function used in assign_taxo_fun.
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`ranomaly::fill_tax_fun` : Secondary function used to complete taxonomy table.
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`ranomaly::check_tax_fun` : Secondary function used to check taxonomy table consistency.
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`ranomaly::generate_phyloseq_fun` : Generate phyloseq object.
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`ranomaly::decontam_fun` : Function to filter phyloseq objects with decontam package features.
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### Diversity analysis
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`ranomaly::rarefaction` : Generate rarefaction curves of each sample.
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`ranomaly::bars_fun` : Generate stacked barplot to visualize community composition.
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`ranomaly::diversity_alpha_fun` : Alpha diversity analysis.
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`ranomaly::diversity_beta_light` : Beta diversity analysis.
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### Differential analysis
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`ranomaly::deseq2_fun` : DESEQ2 Differential Analysis function.
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`ranomaly::metagenomeseq_fun` : metagenomeseq Differential Analysis function.
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`ranomaly::metacoder_fun` : metacoder Differential Analysis function.
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`ranomaly::plsda_fun` : Multivariate methods from mixOmics package for discriminant analysis.
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`ranomaly::aggregate_fun` : Aggregate results of the tree differential analysis methods in one single file.
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`ranomaly::heatmap_fun` : Generate an heatmap with top taxa.
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### Others analysis
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`ranomaly::ASVenn_fun` : Function to create Venn Diagram of shared features.
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`ranomaly::core_soft_fun`: Define core microbiome, soft micriome and transitory microbiome.
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### Utils:
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`ranomaly::phy2tsv_fun` : Export otu table with taxonomy and sequences, + metadata in separated file.
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`ranomaly::subset_fastx` : Allows subset fastq or fasta files at a given threshold.
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`ranomaly::update_metadata_fun` : Update metadata.
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`ranomaly::split_table_fun` : Split phyloseq object.
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`ranomaly::csv2phyloseq_fun` : Create Phyloseq object from external datas.
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`ranomaly::export_to_stamp_fun` : Export to text file to use with STAMP
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`ranomaly::phy2cyto_fun` : Export files for cytoscape.
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`ranomaly::idtaxa_traindb` : IDTAXA db training (idtaxa training functions)
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