From 482e0543d499b7848fcbb8f9f04f60b918096ab8 Mon Sep 17 00:00:00 2001 From: naurasd Date: Mon, 25 Nov 2024 14:08:16 +0000 Subject: [PATCH] deploy: 8bfec127130c91f57cb19b9ed1951d9fe1eb8027 --- .../from_pema/processing_batch1/README.md | 2 +- latest/ro-crate-metadata.json | 144 ++++++++++++++++++ 2 files changed, 145 insertions(+), 1 deletion(-) diff --git a/latest/analysis_data/from_pema/processing_batch1/README.md b/latest/analysis_data/from_pema/processing_batch1/README.md index 29f78b2..ed3e5f1 100644 --- a/latest/analysis_data/from_pema/processing_batch1/README.md +++ b/latest/analysis_data/from_pema/processing_batch1/README.md @@ -3,7 +3,7 @@ In here are the input and output files from the first processing batch of PEMA r The following folders are included here: * [Parameter files](https://github.com/arms-mbon/data_workspace/tree/main/analysis_data/from_pema/processing_batch1/parameter_files): the parameter files used as input for the PEMA runs. * [The taxonomic assignments](https://github.com/arms-mbon/data_workspace/tree/main/analysis_data/from_pema/processing_batch1/taxonomic_assignments): as output by PEMA, containing ASV/OTU read count tables (corrected for ASVs/OTUs occuring in blank samples), ASV/OTU taxonomy assignments and files denoting which ASVs/OTUs got removed/modified because they occurred in blank samples, and a file indicating which samples did not yield any ASVs/OTUs. -* [The taxonomic assignments including data from PCR blanks and omitted samples](https://github.com/arms-mbon/data_workspace/tree/main/analysis_data/from_pema/processing_batch1/taxonomic_assignments_with_blanks): as output by PEMA, containing ASV/OTU raw read count tables including the data of PCR blank samples and the samples which were eventually omitted because they did not produce any ASVs/OTUs. +* [The taxonomic assignments including data from PCR blanks and omitted samples](https://github.com/arms-mbon/data_workspace/tree/main/analysis_data/from_pema/processing_batch1/taxonomic_assignments_with_blanks): as output by PEMA, containing ASV/OTU raw read count tables including the data of PCR blank samples and the samples which were eventually omitted because they had no reads left after blank-correction. * [Curated taxonomic assignments for 18S and COI](https://github.com/arms-mbon/data_workspace/tree/main/analysis_data/from_pema/processing_batch1/updated_taxonomic_assignments): the PEMA taxonomic classification outputs for 18S and COI have been curated: for the first so that we could make a more correct assignment of taxonomic names to those from WoRMS (World Register of Marine Species), for the second to correct a bug in the version of PEMA used. * [The fasta files](https://github.com/arms-mbon/data_workspace/tree/main/analysis_data/from_pema/processing_batch1/fasta): as output by PEMA, containing the sequences of each run. diff --git a/latest/ro-crate-metadata.json b/latest/ro-crate-metadata.json index 169c146..9c8c88d 100644 --- a/latest/ro-crate-metadata.json +++ b/latest/ro-crate-metadata.json @@ -947,6 +947,60 @@ "@type": "Dataset", "label": "./analysis_data/from_pema/processing_batch1/taxonomic_assignments_with_blanks/", "hasPart": [ + { + "@id": "./analysis_data/from_pema/processing_batch1/taxonomic_assignments_with_blanks/Extended_final_table_January2022_18S_withBlank.xlsx" + }, + { + "@id": "./analysis_data/from_pema/processing_batch1/taxonomic_assignments_with_blanks/Extended_final_table_April2021_18S_withBlank.xlsx" + }, + { + "@id": "./analysis_data/from_pema/processing_batch1/taxonomic_assignments_with_blanks/Extended_final_table_April2021_ITS_withBlank.xlsx" + }, + { + "@id": "./analysis_data/from_pema/processing_batch1/taxonomic_assignments_with_blanks/Extended_final_table_May2021_18S_withBlank.xlsx" + }, + { + "@id": 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