finished DEG analysis

NEFSC · Nov 26, 2024 · 5e456e9 · 5e456e9
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commit 5e456e9
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diff --git a/...ysis/Transriptomics/diamond/AirrProDB_CgigNKEGGQuery/blastx_AirrProDB_CgigNKEGGNQuery_out b/...ysis/Transriptomics/diamond/AirrProDB_CgigNKEGGQuery/blastx_AirrProDB_CgigNKEGGNQuery_out
diff --git a/HPC_analysis/Transriptomics/diamond/AirrProDB_CvirgNQuery/blastx_AirrProDB_CvirgNQuery_out b/HPC_analysis/Transriptomics/diamond/AirrProDB_CvirgNQuery/blastx_AirrProDB_CvirgNQuery_out
diff --git a/HPC_analysis/Transriptomics/diamond/GCF_041381155.1_Ai_NY_genomic_ID_REFERENCE.csv b/HPC_analysis/Transriptomics/diamond/GCF_041381155.1_Ai_NY_genomic_ID_REFERENCE.csv
diff --git a/RAnalysis/Data/Transcriptomics/metadata/exp.metadata.csv b/RAnalysis/Data/Transcriptomics/metadata/exp.metadata.csv
@@ -1,41 +1,64 @@
-SampleName_readmatrix,Date,pCO2
-Ai1,20211027,Low
-Ai2,20211027,Low
-Ai3,20211027,Low
-Ai4,20211027,Low
-Ai5,20211027,Low
-Ai6,20211027,Low
-Ai7,20211027,Low
-Ai8,20211027,Low
-Ai9,20211027,Low
-Ai10,20211027,Low
-Ai11,20211027,High
-Ai12,20211027,High
-Ai13,20211027,High
-Ai14,20211027,High
-Ai15,20211027,High
-Ai16,20211027,High
-Ai17,20211027,High
-Ai18,20211027,High
-Ai19,20211027,High
-Ai20,20211027,High
-Ai21,20220228,Low
-Ai22,20220228,Low
-Ai23,20220228,Low
-Ai24,20220228,Low
-Ai25,20220228,Low
-Ai26,20220228,Low
-Ai27,20220228,Low
-Ai28,20220228,Low
-Ai29,20220228,Low
-Ai30,20220228,Low
-Ai31,20220228,High
-Ai32,20220228,High
-Ai33,20220228,High
-Ai34,20220228,High
-Ai35,20220228,High
-Ai36,20220228,High
-Ai37,20220228,High
-Ai38,20220228,High
-Ai39,20220228,High
-Ai40,20220228,High
+SampleName_readmatrix,Date,pCO2,Tank_ID,Gen
+Ai1,20211027,Low,A,F1
+Ai2,20211027,Low,A,F1
+Ai3,20211027,Low,A,F1
+Ai4,20211027,Low,B,F1
+Ai5,20211027,Low,C,F1
+Ai6,20211027,Low,C,F1
+Ai7,20211027,Low,C,F1
+Ai8,20211027,Low,D,F1
+Ai9,20211027,Low,D,F1
+Ai10,20211027,Low,D,F1
+Ai11,20211027,High,A,F1
+Ai12,20211027,High,A,F1
+Ai13,20211027,High,A,F1
+Ai14,20211027,High,B,F1
+Ai15,20211027,High,C,F1
+Ai16,20211027,High,C,F1
+Ai17,20211027,High,C,F1
+Ai18,20211027,High,D,F1
+Ai19,20211027,High,D,F1
+Ai20,20211027,High,D,F1
+Ai21,20220228,Low,A,F1
+Ai22,20220228,Low,B,F1
+Ai23,20220228,Low,C,F1
+Ai24,20220228,Low,D,F1
+Ai25,20220228,Low,E,F1
+Ai26,20220228,Low,E,F1
+Ai27,20220228,Low,F,F1
+Ai28,20220228,Low,G,F1
+Ai29,20220228,Low,G,F1
+Ai30,20220228,Low,H,F1
+Ai31,20220228,High,A,F1
+Ai32,20220228,High,A,F1
+Ai33,20220228,High,B,F1
+Ai34,20220228,High,C,F1
+Ai35,20220228,High,D,F1
+Ai36,20220228,High,E,F1
+Ai37,20220228,High,F,F1
+Ai38,20220228,High,G,F1
+Ai39,20220228,High,H,F1
+Ai40,20220228,High,H,F1
+B11,20221121,High,A,F2
+B12,20221121,High,A,F2
+C1,20221121,High,A,F2
+C2,20221121,High,B,F2
+C3,20221121,High,B,F2
+C4,20221121,High,B,F2
+C5,20221121,High,C,F2
+C6,20221121,High,C,F2
+C7,20221121,High,C,F2
+C8,20221121,High,D,F2
+C9,20221121,High,D,F2
+C10,20221121,High,D,F2
+C11,20221121,Low,A,F2
+C12,20221121,Low,A,F2
+D1,20221121,Low,B,F2
+D2,20221121,Low,B,F2
+D3,20221121,Low,B,F2
+D4,20221121,Low,C,F2
+D5,20221121,Low,C,F2
+D6,20221121,Low,C,F2
+D7,20221121,Low,D,F2
+D8,20221121,Low,D,F2
+D9,20221121,Low,D,F2
diff --git a/RAnalysis/Data/Transcriptomics/metadata/seq_id_AirrCvirg_MERGED_master.csv b/RAnalysis/Data/Transcriptomics/metadata/seq_id_AirrCvirg_MERGED_master.csv
diff --git a/RAnalysis/Output/Transcriptomics/DESeq2/DE_All_Annotation.csv b/RAnalysis/Output/Transcriptomics/DESeq2/DE_All_Annotation.csv
diff --git a/RAnalysis/Output/Transcriptomics/DESeq2/F1_juveniles/F1_DEGs-VolcanoPlot.pdf b/RAnalysis/Output/Transcriptomics/DESeq2/F1_juveniles/F1_DEGs-VolcanoPlot.pdf