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matthewfallan · Feb 3, 2022 · be5a82a · be5a82a
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diff --git a/Analysis/.DS_Store b/Analysis/.DS_Store
diff --git a/Analysis/._.DS_Store b/Analysis/._.DS_Store
diff --git a/Analysis/._23S.dot b/Analysis/._23S.dot
diff --git a/Analysis/._23S.txt b/Analysis/._23S.txt
diff --git a/Analysis/._23S_4V9D.ct b/Analysis/._23S_4V9D.ct
diff --git a/Analysis/._23S_4V9D.ps b/Analysis/._23S_4V9D.ps
diff --git a/Analysis/._23S_4V9D.zip b/Analysis/._23S_4V9D.zip
diff --git a/Analysis/._23S_4V9D_nopk.ps b/Analysis/._23S_4V9D_nopk.ps
diff --git a/Analysis/._23S_4V9D_roc.pdf b/Analysis/._23S_4V9D_roc.pdf
diff --git a/Analysis/._23S_CRW-J01695+pk.dot b/Analysis/._23S_CRW-J01695+pk.dot
diff --git a/Analysis/._23S_CRW-J01695+pk_nesting.tsv b/Analysis/._23S_CRW-J01695+pk_nesting.tsv
diff --git a/Analysis/._23S_CRW-J01695-pk.ps b/Analysis/._23S_CRW-J01695-pk.ps
diff --git a/Analysis/._23S_mus_scatter.png b/Analysis/._23S_mus_scatter.png
diff --git a/Analysis/._23S_vs_rO66v1_sliding.tsv b/Analysis/._23S_vs_rO66v1_sliding.tsv
diff --git a/Analysis/._23S_vs_rO66v1_sliding_dDMS.pdf b/Analysis/._23S_vs_rO66v1_sliding_dDMS.pdf
diff --git a/Analysis/._23S_vs_rO66v1_swarm.pdf b/Analysis/._23S_vs_rO66v1_swarm.pdf
diff --git a/Analysis/._23S_vs_rO66v2_sliding_dDMS.pdf b/Analysis/._23S_vs_rO66v2_sliding_dDMS.pdf
diff --git a/Analysis/._23S_vs_rPB66v1_swarm.pdf b/Analysis/._23S_vs_rPB66v1_swarm.pdf
diff --git a/Analysis/._23S_vs_rPB66v1_violin.pdf b/Analysis/._23S_vs_rPB66v1_violin.pdf
diff --git a/Analysis/._23S_vs_rPB66v2_swarm.pdf b/Analysis/._23S_vs_rPB66v2_swarm.pdf
diff --git a/Analysis/._23S_vs_rPB66v2_violin.pdf b/Analysis/._23S_vs_rPB66v2_violin.pdf
diff --git a/Analysis/._EGFP.dot b/Analysis/._EGFP.dot
diff --git a/Analysis/._M13.dot b/Analysis/._M13.dot
diff --git a/Analysis/._all_origamis_data.csv b/Analysis/._all_origamis_data.csv
diff --git a/Analysis/._analyze_211206.py b/Analysis/._analyze_211206.py
diff --git a/Analysis/._diff_featureless.tsv b/Analysis/._diff_featureless.tsv
diff --git a/Analysis/._dms_by_both_ends_N.pdf b/Analysis/._dms_by_both_ends_N.pdf
diff --git a/Analysis/._dms_by_both_ends_origami_N.pdf b/Analysis/._dms_by_both_ends_origami_N.pdf
diff --git a/Analysis/._dms_by_origami_N.pdf b/Analysis/._dms_by_origami_N.pdf
diff --git a/Analysis/._dms_sig_vs_feature_mean.tsv b/Analysis/._dms_sig_vs_feature_mean.tsv
diff --git a/Analysis/._dms_sig_vs_feature_median.tsv b/Analysis/._dms_sig_vs_feature_median.tsv
diff --git a/Analysis/._feature_ratios.pdf b/Analysis/._feature_ratios.pdf
diff --git a/Analysis/._location_codes.xlsx b/Analysis/._location_codes.xlsx
diff --git a/Analysis/._model_dist-gc_rPB66v1_log_odds_unpaired_summary.txt b/Analysis/._model_dist-gc_rPB66v1_log_odds_unpaired_summary.txt
diff --git a/Analysis/._model_dist-gc_rPB66v1_raw_DMS_summary.txt b/Analysis/._model_dist-gc_rPB66v1_raw_DMS_summary.txt
diff --git a/Analysis/._mus_23S_scatter.png b/Analysis/._mus_23S_scatter.png
diff --git a/Analysis/._origami_data.csv b/Analysis/._origami_data.csv
diff --git a/Analysis/._origami_data_v2-N.csv b/Analysis/._origami_data_v2-N.csv
diff --git a/Analysis/._origami_data_v2-N_use.csv b/Analysis/._origami_data_v2-N_use.csv
diff --git a/Analysis/._origami_data_v2-N_use_R2s.csv b/Analysis/._origami_data_v2-N_use_R2s.csv
diff --git a/Analysis/._origami_data_v2.csv b/Analysis/._origami_data_v2.csv
diff --git a/Analysis/._origami_data_v2_R2s.csv b/Analysis/._origami_data_v2_R2s.csv
diff --git a/Analysis/._rO44v2_distance-GC_volcano.tsv b/Analysis/._rO44v2_distance-GC_volcano.tsv
diff --git a/Analysis/._rO66v1_distance-GC_volcano.pdf b/Analysis/._rO66v1_distance-GC_volcano.pdf
diff --git a/Analysis/._rO66v1_distance-GC_volcano.tsv b/Analysis/._rO66v1_distance-GC_volcano.tsv
diff --git a/Analysis/._rO66v2_distance-GC_volcano.tsv b/Analysis/._rO66v2_distance-GC_volcano.tsv
diff --git a/Analysis/._rO66v2_feature-sequence_volcano.tsv b/Analysis/._rO66v2_feature-sequence_volcano.tsv
diff --git a/Analysis/._rPB66v1_distance-GC_volcano.pdf b/Analysis/._rPB66v1_distance-GC_volcano.pdf
diff --git a/Analysis/._rPB66v1_distance-GC_volcano.tsv b/Analysis/._rPB66v1_distance-GC_volcano.tsv
diff --git a/Analysis/._rPB66v1_feature-sequence_volcano.tsv b/Analysis/._rPB66v1_feature-sequence_volcano.tsv
diff --git a/Analysis/._rPB66v2_distance-GC_volcano.tsv b/Analysis/._rPB66v2_distance-GC_volcano.tsv
diff --git a/Analysis/._rPB66v2_feature-sequence_volcano.tsv b/Analysis/._rPB66v2_feature-sequence_volcano.tsv
diff --git a/Analysis/._rT55_distance-GC_volcano.tsv b/Analysis/._rT55_distance-GC_volcano.tsv
diff --git a/Analysis/._rT55_feature-sequence_volcano.tsv b/Analysis/._rT55_feature-sequence_volcano.tsv
diff --git a/Analysis/._rT66v1_distance-GC_volcano.pdf b/Analysis/._rT66v1_distance-GC_volcano.pdf
diff --git a/Analysis/._rT66v1_distance-GC_volcano.tsv b/Analysis/._rT66v1_distance-GC_volcano.tsv
diff --git a/Analysis/._rT66v1_feature-sequence_volcano.tsv b/Analysis/._rT66v1_feature-sequence_volcano.tsv
diff --git a/Analysis/._rT66v2_distance-GC_volcano.tsv b/Analysis/._rT66v2_distance-GC_volcano.tsv
diff --git a/Analysis/._rT66v2_feature-sequence_volcano.tsv b/Analysis/._rT66v2_feature-sequence_volcano.tsv
diff --git a/Analysis/._rT77_distance-GC_volcano.tsv b/Analysis/._rT77_distance-GC_volcano.tsv
diff --git a/Analysis/._rT77_feature-sequence_volcano.tsv b/Analysis/._rT77_feature-sequence_volcano.tsv
diff --git a/Analysis/._rsc1218v1n660_vs_rT55_sliding.pdf b/Analysis/._rsc1218v1n660_vs_rT55_sliding.pdf
diff --git a/Analysis/._samples.txt.bak b/Analysis/._samples.txt.bak
diff --git a/Analysis/._scaf_scafDX_3-scaf_stapDX_5_dms-vs-pos.pdf b/Analysis/._scaf_scafDX_3-scaf_stapDX_5_dms-vs-pos.pdf
diff --git a/Analysis/._segment_data_N_DMS-all_DMS-int.pdf b/Analysis/._segment_data_N_DMS-all_DMS-int.pdf
diff --git a/Analysis/._segment_data_N_GC_DMS-int.pdf b/Analysis/._segment_data_N_GC_DMS-int.pdf
diff --git a/Analysis/._segment_data_N_GC_DMS_signal.pdf b/Analysis/._segment_data_N_GC_DMS_signal.pdf
diff --git a/Analysis/._segment_data_N_Length_DMS-all.pdf b/Analysis/._segment_data_N_Length_DMS-all.pdf
diff --git a/Analysis/._segment_data_N_Length_DMS-int.pdf b/Analysis/._segment_data_N_Length_DMS-int.pdf
diff --git a/Analysis/._segment_data_N_Length_DMS_signal.pdf b/Analysis/._segment_data_N_Length_DMS_signal.pdf
diff --git a/Analysis/._segment_data_N_Length_GC.pdf b/Analysis/._segment_data_N_Length_GC.pdf
diff --git a/Analysis/._ss_rO66v1.pdf b/Analysis/._ss_rO66v1.pdf
diff --git a/Analysis/._v2-A_distance-GC_volcano.tsv b/Analysis/._v2-A_distance-GC_volcano.tsv
diff --git a/Analysis/._v2-C_distance-GC_volcano.tsv b/Analysis/._v2-C_distance-GC_volcano.tsv
diff --git a/Analysis/._v2-N_distance-GC_volcano.tsv b/Analysis/._v2-N_distance-GC_volcano.tsv
diff --git a/Analysis/.fuse_hidden0000009b00000001 b/Analysis/.fuse_hidden0000009b00000001
diff --git a/Analysis/.ipynb_checkpoints/analyze_220107-checkpoint.ipynb b/Analysis/.ipynb_checkpoints/analyze_220107-checkpoint.ipynb
diff --git a/Analysis/.ipynb_checkpoints/analyze_rO66v1_220122-checkpoint.ipynb b/Analysis/.ipynb_checkpoints/analyze_rO66v1_220122-checkpoint.ipynb
diff --git a/Analysis/23S.ct b/Analysis/23S.ct
diff --git a/Analysis/23S.dot b/Analysis/23S.dot
diff --git a/Analysis/23S.fasta b/Analysis/23S.fasta
@@ -0,0 +1,2 @@
+>23S
+GCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCACGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAATTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGCGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAGGTCCCTCGCGGATGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCA
diff --git a/Analysis/23S.ps b/Analysis/23S.ps
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		@@ -0,0 +1,2 @@
		>23S
		GCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCACGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAATTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGCGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAGGTCCCTCGCGGATGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCA