From 2fa3ff0d06612518570097dd3cbb61fafc74d5ba Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Thu, 6 Feb 2025 16:25:47 +0100
Subject: [PATCH] renamed Metabolomics assay, antiSMASH v6.0 assay added
---
.gitattributes | 1 +
.../README.md | 0
.../dataset/.gitkeep | 0
.../dataset/Table S2.xlsx | 3 +++
.../isa.assay.xlsx | Bin 0 -> 9258 bytes
.../protocols/.gitkeep | 0
.../protocols/BGCAntiSMASH.md | 3 +++
.../isa.assay.xlsx | Bin 11885 -> 11885 bytes
assays/Metabolomics Analysis/README.md | 0
assays/Metabolomics Analysis/dataset/.gitkeep | 0
.../dataset/Metabolomics.md | 0
.../isa.assay.xlsx | Bin 10742 -> 10746 bytes
.../Metabolomics Analysis/protocols/.gitkeep | 0
.../protocols/MetabolomicAnalysis.md | 0
.../isa.assay.xlsx | Bin 11666 -> 11666 bytes
isa.investigation.xlsx | Bin 7876 -> 7876 bytes
.../isa.study.xlsx | Bin 12308 -> 12308 bytes
.../Plant Growth Conditions/isa.study.xlsx | Bin 15939 -> 15939 bytes
18 files changed, 7 insertions(+)
rename assays/{MetabolomicAnalysis => BGC prediction using antiSMASH}/README.md (100%)
rename assays/{MetabolomicAnalysis => BGC prediction using antiSMASH}/dataset/.gitkeep (100%)
create mode 100644 assays/BGC prediction using antiSMASH/dataset/Table S2.xlsx
create mode 100644 assays/BGC prediction using antiSMASH/isa.assay.xlsx
rename assays/{MetabolomicAnalysis => BGC prediction using antiSMASH}/protocols/.gitkeep (100%)
create mode 100644 assays/BGC prediction using antiSMASH/protocols/BGCAntiSMASH.md
create mode 100644 assays/Metabolomics Analysis/README.md
create mode 100644 assays/Metabolomics Analysis/dataset/.gitkeep
rename assays/{MetabolomicAnalysis => Metabolomics Analysis}/dataset/Metabolomics.md (100%)
rename assays/{MetabolomicAnalysis => Metabolomics Analysis}/isa.assay.xlsx (63%)
create mode 100644 assays/Metabolomics Analysis/protocols/.gitkeep
rename assays/{MetabolomicAnalysis => Metabolomics Analysis}/protocols/MetabolomicAnalysis.md (100%)
diff --git a/.gitattributes b/.gitattributes
index fdeb834..6608dce 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -3,3 +3,4 @@
_publication/pnas.2221508120.sapp.pdf filter=lfs diff=lfs merge=lfs -text
_publication/dataverse_files/Table[[:space:]]S2.xlsx filter=lfs diff=lfs merge=lfs -text
assays/Screen[[:space:]]for[[:space:]]antagonistic[[:space:]]interbacterial[[:space:]]interactions/dataset/Table[[:space:]]S2.xlsx filter=lfs diff=lfs merge=lfs -text
+assays/BGC[[:space:]]prediction[[:space:]]using[[:space:]]antiSMASH/dataset/Table[[:space:]]S2.xlsx filter=lfs diff=lfs merge=lfs -text
diff --git a/assays/MetabolomicAnalysis/README.md b/assays/BGC prediction using antiSMASH/README.md
similarity index 100%
rename from assays/MetabolomicAnalysis/README.md
rename to assays/BGC prediction using antiSMASH/README.md
diff --git a/assays/MetabolomicAnalysis/dataset/.gitkeep b/assays/BGC prediction using antiSMASH/dataset/.gitkeep
similarity index 100%
rename from assays/MetabolomicAnalysis/dataset/.gitkeep
rename to assays/BGC prediction using antiSMASH/dataset/.gitkeep
diff --git a/assays/BGC prediction using antiSMASH/dataset/Table S2.xlsx b/assays/BGC prediction using antiSMASH/dataset/Table S2.xlsx
new file mode 100644
index 0000000..3efd1aa
--- /dev/null
+++ b/assays/BGC prediction using antiSMASH/dataset/Table S2.xlsx
@@ -0,0 +1,3 @@
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+size 4062801
diff --git a/assays/BGC prediction using antiSMASH/isa.assay.xlsx b/assays/BGC prediction using antiSMASH/isa.assay.xlsx
new file mode 100644
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diff --git a/assays/MetabolomicAnalysis/protocols/.gitkeep b/assays/BGC prediction using antiSMASH/protocols/.gitkeep
similarity index 100%
rename from assays/MetabolomicAnalysis/protocols/.gitkeep
rename to assays/BGC prediction using antiSMASH/protocols/.gitkeep
diff --git a/assays/BGC prediction using antiSMASH/protocols/BGCAntiSMASH.md b/assays/BGC prediction using antiSMASH/protocols/BGCAntiSMASH.md
new file mode 100644
index 0000000..567d654
--- /dev/null
+++ b/assays/BGC prediction using antiSMASH/protocols/BGCAntiSMASH.md
@@ -0,0 +1,3 @@
+## BGC prediction using antiSMASH
+
+Bacterial genomes were downloaded from “www.at-sphere.com†or NCBI and https://antismash.secondarymetabolites.org/ version 6.0. Output data from antiSMASH analysis are listed as BGC classes and predicted BGCs for each genome in **Table S2**. Only high-quality genomes, as assessed by CheckM with ≥90% completeness and ≤5% contamination ratio were used for the analysis. For R401, the PacBio-sequenced high-quality genome was used for BGC prediction using antiSMASH.
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--
GitLab