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arms-mbon · Mar 26, 2024 · dffc76e · dffc76e
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diff --git a/...nments/Extended_final_table_ARMS_Gdynia_GDY1_20180813_20191029_SF38_DMSO_18S_noBlank.xlsx b/...nments/Extended_final_table_ARMS_Gdynia_GDY1_20180813_20191029_SF38_DMSO_18S_noBlank.xlsx
diff --git a/...nments/Extended_final_table_ARMS_Gdynia_GDY1_20180813_20191029_SF38_DMSO_COI_noBlank.xlsx b/...nments/Extended_final_table_ARMS_Gdynia_GDY1_20180813_20191029_SF38_DMSO_COI_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_April2021_18S_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_April2021_18S_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_April2021_COI_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_April2021_COI_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_April2021_ITS_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_April2021_ITS_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_August2023_18S_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_August2023_18S_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_August2023_COI_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_August2023_COI_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_January2020_18S_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_January2020_18S_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_January2020_COI_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_January2020_COI_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_January2022_18S_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_January2022_18S_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_January2022_COI_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_January2022_COI_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_July2019_18S_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_July2019_18S_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_July2019_COI_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_July2019_COI_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_July2019_ITS_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_July2019_ITS_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_May2021_18S_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_May2021_18S_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_May2021_COI_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_May2021_COI_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_September2020_18S_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_September2020_18S_noBlank.xlsx
diff --git a/taxonomic_assignments/Extended_final_table_September2020_COI_noBlank.xlsx b/taxonomic_assignments/Extended_final_table_September2020_COI_noBlank.xlsx
diff --git a/...assignments/OTUs_ASVs_that_were_removed_modified_because_they_occurred_in_the_blanks.xlsx b/...assignments/OTUs_ASVs_that_were_removed_modified_because_they_occurred_in_the_blanks.xlsx
diff --git a/taxonomic_assignments/README.md b/taxonomic_assignments/README.md
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+Here are the output files containing the taxonomic assignments from the PEMA processing of the ARMS-MBON sequences taken between 2018 and 2020, for the COI, 18S, and ITS marker genes. 
+
+The first chunk of files are "Extended final tables" that contain the following information:
+* an ASV/OTU identifier (these numbers being unique with a single PEMA run)
+* the number of reads for each sample that was processed: each sample is in a separate column, with the title being the material sample ID that can be found in ENA (note: these material sample IDs are not always exactly the same as used in the sampling logsheets in the [sample data folder](https://github.com/arms-mbon/data_workspace/tree/main/qualitycontrolled_data/combined), but they are close)  
+* the full taxonomic classification as returned by the reference database used*
+* the associated NBCI taxon ID (where there is one)
+
+*PEMA v.2.1.4 was used during this processing phase. In this version, for COI gene sequences, the taxonomic classification in these tables stops at the genus level. The species-level classification is not included in the Extended Final Tables. To obtain species-level classification for COI gene sequences, we used the "tax_assignments" files (see below). These files include detailed classifications beyond the genus level for each ASV provided in the Extended Final Tables.
+
+The filenames of the extended final tables contain:
+* the date the samples were sequenced (e.g. April2021)
+* the gene type (e.g. COI)
+* whether or not the blank (sequences) were included
+
+The second chunk of files are the more detailed taxonomic assignements which are produced only for the COI dataset. These contain:
+* an ASV identifier  (these numbers being unique with a single PEMA run; the first part of this ID, before the "_", is included in the ID in the first column of its linked Extended_final_table)
+* For each node of the taxonomic classification: its name and its confidence level
+
+Their filenames contain:
+* the date the samples were sequenced (e.g. April2021)
+* the gene type (e.g. COI)
+
+There is also a file indicating which samples produced [no results](https://github.com/arms-mbon/analysis_release_001/tree/main/taxonomic_assignments/Samples_with_no_results.xlsx) 
+and those which [were removed because they occurred in the blanks](https://github.com/arms-mbon/analysis_release_001/tree/main/taxonomic_assignments/OTUs_ASVs%20that%20were%20removed_modified%20because%20they%20occurred%20in%20the%20blanks.xlsx)
diff --git a/taxonomic_assignments/Samples_with_no_results.xlsx b/taxonomic_assignments/Samples_with_no_results.xlsx
diff --git a/..._assignments/tax_assignments_ARMS_Gdynia_GDY1_20180813_20191029_SF38_DMSO_COI_noBlank.tsv b/..._assignments/tax_assignments_ARMS_Gdynia_GDY1_20180813_20191029_SF38_DMSO_COI_noBlank.tsv
diff --git a/taxonomic_assignments/tax_assignments_April2021_COI_noBlank.tsv b/taxonomic_assignments/tax_assignments_April2021_COI_noBlank.tsv
diff --git a/taxonomic_assignments/tax_assignments_August2023_COI_noBlank.tsv b/taxonomic_assignments/tax_assignments_August2023_COI_noBlank.tsv
diff --git a/taxonomic_assignments/tax_assignments_January2020_COI_noBlank.tsv b/taxonomic_assignments/tax_assignments_January2020_COI_noBlank.tsv
diff --git a/taxonomic_assignments/tax_assignments_January2022_COI_noBlank.tsv b/taxonomic_assignments/tax_assignments_January2022_COI_noBlank.tsv
diff --git a/taxonomic_assignments/tax_assignments_July2019_COI_noBlank.tsv b/taxonomic_assignments/tax_assignments_July2019_COI_noBlank.tsv
diff --git a/taxonomic_assignments/tax_assignments_May2021_COI_noBlank.tsv b/taxonomic_assignments/tax_assignments_May2021_COI_noBlank.tsv
diff --git a/taxonomic_assignments/tax_assignments_September2020_COI_noBlank.tsv b/taxonomic_assignments/tax_assignments_September2020_COI_noBlank.tsv