v0.1 together with MenT1 tutorial

README.md

@@ -42,7 +42,7 @@ We recommend the use a [mamba](https://mamba.readthedocs.io/) (or conda) environ
 * Rsubread 2.16.0
 * Rsamtools 2.16.0
 * DSS 2.48.0
-* vgam 1.1_9
+* VGAM 1.1_9
 * survcomp 1.52.0
 
 

data/MenT1/Msm.reference.tRNAs.with.CCA.fasta

+>Msm.Ala-CGC.trna33 Mycobacterium_smegmatis_MC2_155_chr.trna33-AlaCGC (5550124-5550049)  Ala (CGC) 76 bp  Sc: 83.46
+GGGGCTATGGCGCAGTTGGTAGCGCGACTCGTTCGCATCGAGTAGGTCAGGGGTTCGATTCCCCTTAGCTCCAcca
+>Msm.Ala-GGC.trna9 Mycobacterium_smegmatis_MC2_155_chr.trna9-AlaGGC (2213142-2213214)  Ala (GGC) 73 bp  Sc: 83.13
+GGGGCTATGGCGCAGTTGGTAGCGCACCACACTGGCAGTGTGGGGGTCAGGGGTTCGAATCCCCTTAGCTCCAcca
+>Msm.Ala-TGC.trna2 Mycobacterium_smegmatis_MC2_155_chr.trna2-AlaTGC (10293-10368)  Ala (TGC) 76 bp  Sc: 86.37
+GGGGCCTTAGCTCAGTTGGTAGAGCGCTGCCTTTGCAAGGCAGATGTCAGGAGTTCGAATCTCCTAGGCTCCAcca
+>Msm.Arg-ACG.trna27 Mycobacterium_smegmatis_MC2_155_chr.trna27-ArgACG (6410438-6410366)  Arg (ACG) 73 bp  Sc: 78.03
+GCGCCCGTAGCTCAACGGATAGAGCATCTGACTACGGATCAGAAGGTTAGGGGTTCGAATCCCTTCGGGCGCAcca
+>Msm.Arg-TCT.trna15 Mycobacterium_smegmatis_MC2_155_chr.trna15-ArgTCT (4797480-4797552)  Arg (TCT) 73 bp  Sc: 74.64
+GCCTCCGTAGCTCAATGGATAGAGCATCGGCCTTCTAATCCGACGGTTGCAGGTTCGAGTCCTGCCGGGGGCGcca
+>Msm.Arg-CCG.trna18 Mycobacterium_smegmatis_MC2_155_chr.trna18-ArgCCG (5058252-5058327)  Arg (CCG) 76 bp  Sc: 78.92
+GCCCCCGTAGCTCAGGGGATAGAGCGTCTGCCTCCGGAGCAGAAGGCCGCAGGTTCGAATCCTGCCGGGGGCAcca
+>Msm.Arg-CCT.trna20 Mycobacterium_smegmatis_MC2_155_chr.trna20-ArgCCT (5685927-5685999)  Arg (CCT) 73 bp  Sc: 74.23
+GCCCTCGTAGCTCAGGGGATAGAGCACGGCTCTCCTAAAGCCGGTGTCGCAGGTTCGAATCCTGCCGGGGGCAcca
+>Msm.Asn-GTT.trna37 Mycobacterium_smegmatis_MC2_155_chr.trna37-AsnGTT (4561282-4561207)  Asn (GTT) 76 bp  Sc: 79.73
+TCCCCTGTAGCTCAATTGGCAGAGCATTCGGCTGTTAACCGAAGGGTTGCTGGTTCGAGTCCAGCCGGGGGAGcca
+>Msm.Asp-GTC.trna31 Mycobacterium_smegmatis_MC2_155_chr.trna31-AspGTC (5834285-5834209)  Asp (GTC) 77 bp  Sc: 94.44
+GGCCCTGTGGCGCAGTTGGTTAGCGCGCCGCCCTGTCACGGCGGAGGTCGCGGGTTCAAGTCCCGTCAGGGTCGCCA
+>Msm.Cys-GCA.trna40 Mycobacterium_smegmatis_MC2_155_chr.trna40-CysGCA (3883718-3883645)  Cys (GCA) 74 bp  Sc: 57.51
+GCGGGTGTGGCTGAGTGGCTAGGCAGCGGCCTGCAAAGCCGTCTACACGGGTTCGAGTCCCGTCACTCGCTcca
+>Msm.Cys-GCA.trna44 Mycobacterium_smegmatis_MC2_155_chr.trna44-CysGCA (2895245-2895172)  Cys (GCA) 74 bp  Sc: 76.31
+GGTGGAGTGGCCGAGTGGTGAGGCAACGGCCTGCAAAGCCGTGCACACGGGTTCGATTCCCGTCTCCACCTCCA
+>Msm.Gln-CTG.trna10 Mycobacterium_smegmatis_MC2_155_chr.trna10-GlnCTG (2467984-2468058)  Gln (CTG) 75 bp  Sc: 64.27
+TGGGGTATGGTGTAATTGGCAACACAGCTGATTCTGGTTCAGCCATTCTAGGTTCGAGTCCTGGTACCCCAGCCA
+>Msm.Gln-TTG.trna19 Mycobacterium_smegmatis_MC2_155_chr.trna19-GlnTTG (5509404-5509475)  Gln (TTG) 72 bp  Sc: 49.46
+TCCGTCGTGGTGTAATCGGCAGCACCTCTGATTTTGGTTCAGATAGTTCAGGTTCGAGTCCTGGCGACGGAGcca
+>Msm.Glu-CTC.trna11 Mycobacterium_smegmatis_MC2_155_chr.trna11-GluCTC (2468127-2468202)  Glu (CTC) 76 bp  Sc: 61.50
+GCCCCCGTCGTCTAGCGGCCTAGGACGCCGCCCTCTCACGGCGGTAGCGTGGGTTCGAATCCCATCGGGGGTAcca
+>Msm.Glu-TTC.trna30 Mycobacterium_smegmatis_MC2_155_chr.trna30-GluTTC (5834394-5834322)  Glu (TTC) 73 bp  Sc: 62.82
+GCCCCCATCGTCTAGTGGCCTAGGACGCCGCCCTTTCACGGCGGTAGCACGGGTTCGAATCCCGTTGGGGGTAcca
+>Msm.Gly-CCC.trna47 Mycobacterium_smegmatis_MC2_155_chr.trna47-GlyCCC (760074-760001)  Gly (CCC) 74 bp  Sc: 81.73
+GCCGGTGTAGTTCAATGGCAGAACATCAGCTTCCCAAGCTGAATACGCGGGTTCGATTCCCGTCACCGGCTCCA
+>Msm.Gly-GCC.trna43 Mycobacterium_smegmatis_MC2_155_chr.trna43-GlyGCC (2895346-2895271)  Gly (GCC) 76 bp  Sc: 89.46
+GCGGATGTAGCGCAGTTGGTAGCGCATCACCTTGCCAAGGTGAGGGTCGCGGGTTCGAATCCCGTCATCCGCTcca
+>Msm.Gly-TCC.trna14 Mycobacterium_smegmatis_MC2_155_chr.trna14-GlyTCC (4764493-4764563)  Gly (TCC) 71 bp  Sc: 72.19
+GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTcca
+>Msm.His-GTG.trna16 Mycobacterium_smegmatis_MC2_155_chr.trna16-HisGTG (4817832-4817907)  His (GTG) 76 bp  Sc: 77.37
+GTGGCTGTAGTTCAGTTGGTAGAGCACCAGGTTGTGATCCTGGCTGTCGCGGGTTCGAGTCCCGTCAGCCACCcca
+>Msm.Ile-GAT.trna1 Mycobacterium_smegmatis_MC2_155_chr.trna1-IleGAT (10072-10148)  Ile (GAT) 77 bp  Sc: 88.31
+GGGCCTATAGCTCAGGCGGTTAGAGCGCTTCGCTGATAACGAAGAGGTCGGAGGTTCGAGTCCTCCTAGGCCCAcca
+>Msm.Leu-CAA.trna42 Mycobacterium_smegmatis_MC2_155_chr.trna42-LeuCAA (3328766-3328690)  Leu (CAA) 77 bp  Sc: 53.44
+GCCCTCGTATCCCAACTGGCAGAGGAAACGGATTCAAAACCCGTACAGTGTGAGTTCGAATCTCACCGAGGGCACCA
+>Msm.Leu-CAG.trna3 Mycobacterium_smegmatis_MC2_155_chr.trna3-LeuCAG (58144-58226)  Leu (CAG) 83 bp  Sc: 63.75
+GGGCGAGTGGCGGAATGGCAGACGCGCTGGCTTCAGGTGCCAGTGTCCTTCGGGACGTGGGGGTTCAAGTCCCCCTTCGCCCAcca
+>Msm.Leu-GAG.trna13 Mycobacterium_smegmatis_MC2_155_chr.trna13-LeuGAG (4278994-4279079)  Leu (GAG) 86 bp  Sc: 60.48
+GTCCGAGTGGCGGAATGGCAGACGCGCTAGCTTGAGGTGCTAGTGCCCTATTAACGGGCGTGGGGGTTCAAGTCCCCCCTCGGACAcca
+>Msm.Leu-TAA.trna34 Mycobacterium_smegmatis_MC2_155_chr.trna34-LeuTAA (5458984-5458911)  Leu (TAA) 74 bp  Sc: 63.84
+GCCCCCATAGCCCAATTGGCAGAGGCAGCGGACTTAAAATCCGCCAAGTGTCGGTTCGAGTCCGACTGGGGGCAcca
+>Msm.Leu-TAG.trna35 Mycobacterium_smegmatis_MC2_155_chr.trna35-LeuTAG (4992927-4992841)  Leu (TAG) 87 bp  Sc: 65.79
+GCGGGCGTGGCGAAATCGGTATACGCGCGGGTTTTAGGTGCCCGTGTTCGAGAGAACGTGTGGGTTCGAGTCCCACCGCCCGCACCA
+>Msm.Lys-CTT.trna17 Mycobacterium_smegmatis_MC2_155_chr.trna17-LysCTT (4847908-4847983)  Lys (CTT) 76 bp  Sc: 91.80
+GCGCCGTTAGCTCAGTTGGTAGAGCAGCTGACTCTTAATCAGCGGGTCCGGGGTTCGAAACCCTGACGGCGCACCA
+>Msm.Lys-TTT.trna21 Mycobacterium_smegmatis_MC2_155_chr.trna21-LysTTT (5834573-5834645)  Lys (TTT) 73 bp  Sc: 79.21
+GCCCCTATAGCTCAGTTGGTAGAGCTACGGACTTTTAATCCGCAGGTCCCAGGTTCGAGCCCTGGTGGGGGCAcca
+>Msm.Met-CAT.trna8 Mycobacterium_smegmatis_MC2_155_chr.trna8-MetCAT (2047596-2047672)  Met (CAT) 77 bp  Sc: 81.09
+CGCGGGGTGGAGCAGCTCGGTAGCTCGCTGGGCTCATAACCCAGAGGTCGCAGGTTCGAATCCTGTCCCCGCTAcca
+>Msm.Met-CAT.trna6 Mycobacterium_smegmatis_MC2_155_chr.trna6-MetCAT (1436094-1436167)  Met (CAT) 74 bp  Sc: 82.06
+GGCGGTGTAGCTCAGCTGGTTAGAGCGCACGACTCATAATCGTGAGGTCGGGGGATCGAGCCCCCCCACCGCTAcca
+>Msm.Met-CAT.trna38 Mycobacterium_smegmatis_MC2_155_chr.trna38-MetCAT (4532894-4532821)  Met (CAT) 74 bp  Sc: 85.15
+GGGGCGGTAGCTCAGTCGGTTAGAGCCGCGGACTCATAATCCGCTGGTCGCGGGTTCGAGCCCCGCCCGCCCTAcca
+>Msm.Phe-GAA.trna32 Mycobacterium_smegmatis_MC2_155_chr.trna32-PheGAA (5834167-5834094)  Phe (GAA) 74 bp  Sc: 83.44
+GGCCAGGTAGCTCAGTTGGTACGAGCGTCCGCCTGAAAAGCGGAAGGTCGCCGGTTCGATCCCGGCCCTGGCCAcca
+>Msm.Pro-CGG.trna23 Mycobacterium_smegmatis_MC2_155_chr.trna23-ProCGG (6272367-6272440)  Pro (CGG) 74 bp  Sc: 81.26
+CGGGGTGTGGCGCAGCTTGGTAGCGCGCTTCGTTCGGGACGAAGAGGTCGTGGGTTCGAATCCCGCCACCCCGAcca
+>Msm.Pro-GGG.trna41 Mycobacterium_smegmatis_MC2_155_chr.trna41-ProGGG (3800622-3800546)  Pro (GGG) 77 bp  Sc: 79.60
+CGGGCTGTGGCGCAGCTTGGTAGCGCACTTGACTGGGGGTCAAGTGGTCGCAGGTTCAAATCCTGTCAGCCCGAcca
+>Msm.Pro-TGG.trna36 Mycobacterium_smegmatis_MC2_155_chr.trna36-ProTGG (4764371-4764298)  Pro (TGG) 74 bp  Sc: 81.49
+CGGGGTGTAGCGCAGCTTGGTAGCGCATCCGCTTTGGGAGCGGAAGGCCGCAGGTTCAAATCCTGTCACCCCGAcca
+>Msm.SeC-TCA.trna46 Mycobacterium_smegmatis_MC2_155_chr.trna46-SeCTCA (1928522-1928428)  SeC (TCA) 95 bp  Sc: 30.05
+GGAGGCGTATCCGGTCTGGTGACCGGCGCGGTCTTCAAAATCGCTGAGCGACAGTTTCTGCCGCTGGCGGGTTCGATTCCCGTCCGCCTCCGCCA
+>Msm.Ser-CGA.trna28 Mycobacterium_smegmatis_MC2_155_chr.trna28-SerCGA (6393912-6393822)  Ser (CGA) 91 bp  Sc: 68.85
+GGTGGCGTGTCCGAGCGGCCTAAGGAGCACGCCTCGAAAGCGTGTGTGGGGTAACCCCCCACCGAGGGTTCAAATCCCTCCGCCACCGCCA
+>Msm.Ser-GCT.trna26 Mycobacterium_smegmatis_MC2_155_chr.trna26-SerGCT (6410567-6410476)  Ser (GCT) 92 bp  Sc: 67.19
+GGAGGCGTGCCAGAGCGGCCGAATGGGACTCACTGCTAATGAGTTGTCCCCCTTACCGGGGACCGGAGGTTCAAATCCTCTCGCCTCCGCCA
+>Msm.Ser-GGA.trna24 Mycobacterium_smegmatis_MC2_155_chr.trna24-SerGGA (6352992-6353077)  Ser (GGA) 86 bp  Sc: 56.71
+GGAGGATTCGCCTAGTGGCCTATGGCGCTCGCCTGGAACGCGGGTTGGGTTAATAGCCCTCGCGGGTTCAAATCCCGCATCCTCCGcca
+>Msm.Ser-TGA.trna25 Mycobacterium_smegmatis_MC2_155_chr.trna25-SerTGA (6417776-6417690)  Ser (TGA) 87 bp  Sc: 65.11
+GGTGGCGTGGCAGAGCGGCCTAATGCACTCGCCTTGAAAGCGAGAGACGGCTAACACCGTCCGGGGGTTCAAATCCCTCCGCCACCGcca
+>Msm.Thr-CGT.trna29 Mycobacterium_smegmatis_MC2_155_chr.trna29-ThrCGT (6221063-6220991)  Thr (CGT) 73 bp  Sc: 86.49
+GCCGCCTTAGCTCAGTCGGTAGAGCGATTCACTCGTAATGAATAGGTCGGGGGTTCGATTCCCCCAGGCGGCTcca
+>Msm.Thr-GGT.trna5 Mycobacterium_smegmatis_MC2_155_chr.trna5-ThrGGT (1435983-1436055)  Thr (GGT) 73 bp  Sc: 77.85
+GCCCCCTTAGCTCAGTCGGCAGAGCGTTTCCATGGTAAGGAAAAGGTCAACGGTTCGATTCCGTTAGGGGGCTcca
+>Msm.Thr-TGT Thr (TGT) 75 bp  Sc: 85.47
+GCCTCCTTAGCTCAGTGGTAGAGCACTCGCCTTGTAAGCGAGCGGTCGTCAGTTCAATCCTGACAGGGGGCTCCA
+>Msm.Trp-CCA.trna7 Mycobacterium_smegmatis_MC2_155_chr.trna7-TrpCCA (1437965-1438037)  Trp (CCA) 73 bp  Sc: 80.23
+AGGGGCGTAGCTCAATTGGCAGAGCAGCGGTCTCCAAAACCGCAGGTTGCAGGTTCAAGTCCTGTCGCCCCTGcca
+>Msm.Tyr-GTA.trna4 Mycobacterium_smegmatis_MC2_155_chr.trna4-TyrGTA (1228393-1228478)  Tyr (GTA) 86 bp  Sc: 56.35
+GGCAGGTTGCCCGAGCGGCCAATGGGAGCGGACTGTAAATCCGTCGGCTAACGCCTACGCAGGTTCGAATCCTGCACCTGCCAcca
+>Msm.Val-CAC.trna12 Mycobacterium_smegmatis_MC2_155_chr.trna12-ValCAC (2895813-2895887)  Val (CAC) 75 bp  Sc: 87.83
+GGTCTCGTAGCTCAGTGGGAGAGCGTCCGCCTCACACGCGGAAGGTCGCTGGTTCGAACCCAGCCGGGACCACCA
+>Msm.Val-GAC.trna45 Mycobacterium_smegmatis_MC2_155_chr.trna45-ValGAC (2895160-2895086)  Val (GAC) 75 bp  Sc: 87.89
+GCGCGATTAGCTCAGCGGGAGAGCGCTTCCCTGACACGGAAGAGGTCACTGGTTCAATCCCAGTATCGCGCACCA
+>Msm.Val-TAC.trna39 Mycobacterium_smegmatis_MC2_155_chr.trna39-ValTAC (4405846-4405775)  Val (TAC) 72 bp  Sc: 75.84
+GGGCGCGTAGCTCAGTGGTAGAGCTCTGGTTTTACACACCAGCGGTCGGCGGTTCGATACCGTCCGCGCCCAccacca

src/emote-tk-shared-env-R4.3.2.txt

+r-base=4.3.2
+r-tidyverse=2.0.0
+r-dt=0.31
+bioconductor-biostrings=2.68.1
+bioconductor-rsubread=2.16.0
+bioconductor-rbowtie=1.42.0
+bioconductor-shortread=1.58.0
+bioconductor-rsamtools=2.16.0
+r-vgam=1.1_9
+bioconductor-survcomp=1.52.0
+bioconductor-dss=2.48.0