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arms-mbon · Nov 25, 2024 · 482e054 · 482e054
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diff --git 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
@@ -947,6 +947,60 @@
             "@type": "Dataset",
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+                },
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+                },
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+                },
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+                },
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+                },
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+                },
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+                },
+                {
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+                },
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+                },
                 {
                     "@id": "./analysis_data/from_pema/processing_batch1/taxonomic_assignments_with_blanks/README.md"
                 }
@@ -2331,6 +2385,96 @@
             "@type": "File",
             "label": "./reformatted_data/README.md"
         },
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