initial commit HIV_samples

owlang · owlang · commit f2873a99be2c · 2021-10-13T10:43:56.000-04:00
This commit includes the initial READMEs to outline the directory structure of this directory along with the HIV genome used (saved to input) and the updated setup.sh script for creating a new hg19-based EpitopeID database that includes the HIV genome as an "epitope"/"FASTA_Tag".
diff --git a/paper/HIV_samples/README b/paper/HIV_samples/README
@@ -0,0 +1,11 @@
+# Run EpitopeID on HIV datasets to evaluate EpitopeID's ability to detect HIV genome insertions
+
+# "Benzotriazoles Reactivate Latent HIV-1 through Inactivation of STAT5 SUMOylation"
+# (Bosque et al, 2017)
+
+# GEO accession: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84199
+# HIV genome: https://www.ncbi.nlm.nih.gov/nuccore/AF324493
+
+# EpitopeID database with HIV genome as a tag and hg19 genome as genomic sequence is setup with `../setup.sh`
+# Download data using SRA accessions using `job/00_download_data.pbs`
+# Run EpitopeID on FASTQ inputs using `job/01_run_EpitopeID.pbs` to determine if EpitopeID can localize HIV genome insertions
diff --git a/paper/HIV_samples/logs/README b/paper/HIV_samples/logs/README
@@ -0,0 +1 @@
+# logfiles from STDERR and STDOUT of running job files go here
diff --git a/paper/HIV_samples/results/README b/paper/HIV_samples/results/README
@@ -0,0 +1 @@
+# Downloaded FASTQ files and EpitopeID results go here
diff --git a/paper/README b/paper/README
@@ -14,6 +14,7 @@ paper
 |--SyntheticDeletion
 |--ENCODEdata-eGFP
 |--ENCODEdata-CellLines
+|--HIV_samples
 |--YKOC-wgs
 
 
@@ -47,5 +48,8 @@ contains the scripts and information for downloading ENCODE eGFP data to test Ep
 ## ENCODEdata-CellLines
 contains the scripts and information for downloading ENCODE transcription factor ChIP-seq data to test StrainID
 
+## HIV_samples
+contains the scripts and information for downloading, processing, and running EpitopeID on the Bosque et al, 2017 dataset for localizing HIV genome insertions
+
 ## YKOC-wgs
 contains the scripts and information for downloading, processing, and running DeletionID on the Puddu et al, 2019 dataset for identifying deletions
diff --git a/paper/input/AF324493.2_HIV-1_vector_pNL4-3.fa b/paper/input/AF324493.2_HIV-1_vector_pNL4-3.fa
@@ -0,0 +1,214 @@
+>AF324493.2 HIV-1 vector pNL4-3, complete sequence
+TGGAAGGGCTAATTTGGTCCCAAAAAAGACAAGAGATCCTTGATCTGTGGATCTACCACACACAAGGCTA
+CTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTTC
+AAGTTAGTACCAGTTGAACCAGAGCAAGTAGAAGAGGCCAATGAAGGAGAGAACAACAGCTTGTTACACC
+CTATGAGCCAGCATGGGATGGAGGACCCGGAGGGAGAAGTATTAGTGTGGAAGTTTGACAGCCTCCTAGC
+ATTTCGTCACATGGCCCGAGAGCTGCATCCGGAGTACTACAAAGACTGCTGACATCGAGCTTTCTACAAG
+GGACTTTCCGCTGGGGACTTTCCAGGGAGGTGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGAT
+GCTACATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGC
+TCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCAAAGTAGTGTG
+TGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCT
+AGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGTAAAGCCAGAGGAGATCTCTCGACGCAGGACTCG
+GCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGC
+GGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCGGTATTAAGCGGGGGAGAATTAGATAAATGGGAA
+AAAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAACTAAAACATATAGTATGGGCAAGCAGGGAGC
+TAGAACGATTCGCAGTTAATCCTGGCCTTTTAGAGACATCAGAAGGCTGTAGACAAATACTGGGACAGCT
+ACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTATTGT
+GTGCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCCTTAGATAAGATAGAGGAAGAGCAAAACAAAA
+GTAAGAAAAAGGCACAGCAAGCAGCAGCTGACACAGGAAACAACAGCCAGGTCAGCCAAAATTACCCTAT
+AGTGCAGAACCTCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAA
+GTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCC
+CACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGAC
+CATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAG
+ATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGA
+CACATAATCCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGT
+AAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTA
+GACCGATTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAAGAGGTAAAAAATTGGATGACAGAAACCT
+TGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGGAGCGACACTAGA
+AGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATG
+AGCCAAGTAACAAATCCAGCTACCATAATGATACAGAAAGGCAATTTTAGGAACCAAAGAAAGACTGTTA
+AGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTG
+GAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATC
+TGGCCTTCCCACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAG
+AGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTA
+TCCTTTAGCTTCCCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAAGATAGGGGGGCAATTAA
+AGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAA
+ACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATC
+TGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGT
+TGACTCAGATTGGCTGCACTTTAAATTTTCCCATTAGTCCTATTGAGACTGTACCAGTAAAATTAAAGCC
+AGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATT
+TGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTAT
+TTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAAC
+TCAAGATTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAACAGAAAAAATCAGTAACA
+GTACTGGATGTGGGCGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAGTATACTGCATTTA
+CCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAA
+AGGATCACCAGCAATATTCCAGTGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGAC
+ATAGTCATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAA
+AAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGA
+ACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCA
+GAAAAGGACAGCTGGACTGTCAATGACATACAGAAATTAGTGGGAAAATTGAATTGGGCAAGTCAGATTT
+ATGCAGGGATTAAAGTAAGGCAATTATGTAAACTTCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACC
+ACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAACCGGTACATGGAGTG
+TATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAA
+TTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAGTATGCAAGAATGAAGGGTGCCCACACTAATGA
+TGTGAAACAATTAACAGAGGCAGTACAAAAAATAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCT
+AAATTTAAATTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGCAAGCCACCTGGA
+TTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAGTTATGGTACCAGTTAGAGAAAGAACCCAT
+AATAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCCAATAGGGAAACTAAATTAGGAAAAGCAGGATAT
+GTAACTGACAGAGGAAGACAAAAAGTTGTCCCCCTAACGGACACAACAAATCAGAAGACTGAGTTACAAG
+CAATTCATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTGACAGACTCACAATATGCATTGGG
+AATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTCAGTCAAATAATAGAGCAGTTAATAAAA
+AAGGAAAAAGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAAT
+TGGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGAAGAACATGAGAA
+ATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTACCACCTGTAGTAGCAAAAGAAATAGTA
+GCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATGCATGGACAAGTAGACTGTAGCCCAGGAATAT
+GGCAGCTAGATTGTACACATTTAGAAGGAAAAGTTATCTTGGTAGCAGTTCATGTAGCCAGTGGATATAT
+AGAAGCAGAAGTAATTCCAGCAGAGACAGGGCAAGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGA
+TGGCCAGTAAAAACAGTACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTT
+GGTGGGCGGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAATAGAATCTAT
+GAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAA
+ATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAG
+TAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCG
+GGTTTATTACAGGGACAGCAGAGATCCAGTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGG
+GCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATCAGGGATT
+ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAACACATGGAAAAGAT
+TAGTAAAACACCATATGTATATTTCAAGGAAAGCTAAGGACTGGTTTTATAGACATCACTATGAAAGTAC
+TAATCCAAAAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAAATTAGTAATAACAACATATTGG
+GGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGAT
+ATAGCACACAAGTAGACCCTGACCTAGCAGACCAACTAATTCATCTGCACTATTTTGATTGTTTTTCAGA
+ATCTGCTATAAGAAATACCATATTAGGACGTATAGTTAGTCCTAGGTGTGAATATCAAGCAGGACATAAC
+AAGGTAGGATCTCTACAGTACTTGGCACTAGCAGCATTAATAAAACCAAAACAGATAAAGCCACCTTTGC
+CTAGTGTTAGGAAACTGACAGAGGACAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCA
+TACAATGAATGGACACTAGAGCTTTTAGAGGAACTTAAGAGTGAAGCTGTTAGACATTTTCCTAGGATAT
+GGCTCCATAACTTAGGACAACATATCTATGAAACTTACGGGGATACTTGGGCAGGAGTGGAAGCCATAAT
+AAGAATTCTGCAACAACTGCTGTTTATCCATTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACT
+CGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAG
+CCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATGACAA
+AAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGAC
+TCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATAATAGTAGCAATAGTAGCA
+TTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAA
+GACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGA
+AGGAGAAGTATCAGCACTTGTGGAGATGGGGGTGGAAATGGGGCACCATGCTCCTTGGGATATTGATGAT
+CTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACC
+ACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCT
+GTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAA
+AAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTA
+AAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTA
+GCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGA
+TAAGGTGCAGAAAGAATATGCATTCTTTTATAAACTTGATATAGTACCAATAGATAATACCAGCTATAGG
+TTGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATAC
+ATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATG
+TACAAATGTCAGCACAGTACAATGTACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTAAAT
+GGCAGTCTAGCAGAAGAAGATGTAGTAATTAGATCTGCCAATTTCACAGACAATGCTAAAACCATAATAG
+TACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATCCGTAT
+CCAGAGGGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAAC
+ATTAGTAGAGCAAAATGGAATGCCACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATA
+ATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGG
+AGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACT
+GAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACACTCCCATGCAGAATAAAACAATTTATAAACA
+TGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATAT
+TACTGGGCTGCTATTAACAAGAGATGGTGGTAATAACAACAATGGGTCCGAGATCTTCAGACCTGGAGGA
+GGCGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAG
+TAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTT
+CCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCCAGA
+CAATTATTGTCTGATATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGT
+TGCAACTCACAGTCTGGGGCATCAAACAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGA
+TCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCT
+AGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATAACATGACCTGGATGGAGTGGGACAGAGAAATTA
+ACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGA
+ATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATA
+AAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGA
+ATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAATCCCGAGGGGACCCGACAG
+GCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC
+TTAGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCT
+TGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCT
+CCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAACTTGCTCAATGCCACAGCCATAGCAGTA
+GCTGAGGGGACAGATAGGGTTATAGAAGTATTACAAGCAGCTTATAGAGCTATTCGCCACATACCTAGAA
+GAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTG
+GATGGCCTGCTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATGGGGTGGGAGCAGTATCTCG
+AGACCTAGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTAACAATGCTGCTTGTGCCTGGCTA
+GAAGCACAAGAGGAGGAAGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACA
+AGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAG
+AAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACA
+CCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATA
+AGGTAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGA
+CCCTGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTG
+CATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAG
+GGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTTG
+CCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACT
+GCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGT
+AACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCACCCAGGAGGTAGAGGTTGCAG
+TGAGCCAAGATCGCGCCACTGCATTCCAGCCTGGGCAAGAAAACAAGACTGTCTAAAATAATAATAATAA
+GTTAAGGGTATTAAATATATTTATACATGGAGGTCATAAAAATATATATATTTGGGCTGGGCGCAGTGGC
+TCACACCTGCGCCCGGCCCTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGTTTGGGAGTTCCAGACCAG
+CCTGACCAACATGGAGAAACCCCTTCTCTGTGTATTTTTAGTAGATTTTATTTTATGTGTATTTTATTCA
+CAGGTATTTCTGGAAAACTGAAACTGTTTTTCCTCTACTCTGATACCACAAGAATCATCAGCACAGAGGA
+AGACTTCTGTGATCAAATGTGGTGGGAGAGGGAGGTTTTCACCAGCACATGAGCAGTCAGTTCTGCCGCA
+GACTCGGCGGGTGTCCTTCGGTTCAGTTCCAACACCGCCTGCCTGGAGAGAGGTCAGACCACAGGGTGAG
+GGCTCAGTCCCCAAGACATAAACACCCAAGACATAAACACCCAACAGGTCCACCCCGCCTGCTGCCCAGG
+CAGAGCCGATTCACCAAGACGGGAATTAGGATAGAGAAAGAGTAAGTCACACAGAGCCGGCTGTGCGGGA
+GAACGGAGTTCTATTATGACTCAAATCAGTCTCCCCAAGCATTCGGGGATCAGAGTTTTTAAGGATAACT
+TAGTGTGTAGGGGGCCAGTGAGTTGGAGATGAAAGCGTAGGGAGTCGAAGGTGTCCTTTTGCGCCGAGTC
+AGTTCCTGGGTGGGGGCCACAAGATCGGATGAGCCAGTTTATCAATCCGGGGGTGCCAGCTGATCCATGG
+AGTGCAGGGTCTGCAAAATATCTCAAGCACTGATTGATCTTAGGTTTTACAATAGTGATGTTACCCCAGG
+AACAATTTGGGGAAGGTCAGAATCTTGTAGCCTGTAGCTGCATGACTCCTAAACCATAATTTCTTTTTTG
+TTTTTTTTTTTTTATTTTTGAGACAGGGTCTCACTCTGTCACCTAGGCTGGAGTGCAGTGGTGCAATCAC
+AGCTCACTGCAGCCTCAACGTCGTAAGCTCAAGCGATCCTCCCACCTCAGCCTGCCTGGTAGCTGAGACT
+ACAAGCGACGCCCCAGTTAATTTTTGTATTTTTGGTAGAGGCAGCGTTTTGCCGTGTGGCCCTGGCTGGT
+CTCGAACTCCTGGGCTCAAGTGATCCAGCCTCAGCCTCCCAAAGTGCTGGGACAACCGGGGCCAGTCACT
+GCACCTGGCCCTAAACCATAATTTCTAATCTTTTGGCTAATTTGTTAGTCCTACAAAGGCAGTCTAGTCC
+CCAGGCAAAAAGGGGGTTTGTTTCGGGAAAGGGCTGTTACTGTCTTTGTTTCAAACTATAAACTAAGTTC
+CTCCTAAACTTAGTTCGGCCTACACCCAGGAATGAACAAGGAGAGCTTGGAGGTTAGAAGCACGATGGAA
+TTGGTTAGGTCAGATCTCTTTCACTGTCTGAGTTATAATTTTGCAATGGTGGTTCAAAGACTGCCCGCTT
+CTGACACCAGTCGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCT
+TCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAA
+AGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCA
+AAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCAT
+CACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCC
+CTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCC
+TTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCC
+AAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTG
+AGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAG
+GTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTT
+GGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAA
+CCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGA
+AGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTC
+ATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAA
+GTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTG
+TCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCA
+TCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACC
+AGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTG
+TTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGC
+ATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTA
+CATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTT
+GGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGA
+TGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCT
+CTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAA
+ACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGT
+GCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAA
+ATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTA
+TTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAA
+ATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACAT
+TAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTCGCGCGTTTCGGTGATGACGGTGAAAACCT
+CTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGT
+CAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCTGGCTTAACTATGCGGCATCAGAGCAGATTGTAC
+TGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCCA
+TTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGGGG
+AGGCAGAGATTGCAGTAAGCTGAGATCGCAGCACTGCACTCCAGCCTGGGCGACAGAGTAAGACTCTGTC
+TCAAAAATAAAATAAATAAATCAATCAGATATTCCAATCTTTTCCTTTATTTATTTATTTATTTTCTATT
+TTGGAAACACAGTCCTTCCTTATTCCAGAATTACACATATATTCTATTTTTCTTTATATGCTCCAGTTTT
+TTTTAGACCTTCACCTGAAATGTGTGTATACAAAATCTAGGCCAGTCCAGCAGAGCCTAAAGGTAAAAAA
+TAAAATAATAAAAAATAAATAAAATCTAGCTCACTCCTTCACATCAAAATGGAGATACAGCTGTTAGCAT
+TAAATACCAAATAACCCATCTTGTCCTCAATAATTTTAAGCGCCTCTCTCCACCACATCTAACTCCTGTC
+AAAGGCATGTGCCCCTTCCGGGCGCTCTGCTGTGCTGCCAACCAACTGGCATGTGGACTCTGCAGGGTCC
+CTAACTGCCAAGCCCCACAGTGTGCCCTGAGGCTGCCCCTTCCTTCTAGCGGCTGCCCCCACTCGGCTTT
+GCTTTCCCTAGTTTCAGTTACTTGCGTTCAGCCAAGGTCTGAAACTAGGTGCGCACAGAGCGGTAAGACT
+GCGAGAGAAAGAGACCAGCTTTACAGGGGGTTTATCACAGTGCACCCTGACAGTCGTCAGCCTCACAGGG
+GGTTTATCACATTGCACCCTGACAGTCGTCAGCCTCACAGGGGGTTTATCACAGTGCACCCTTACAATCA
+TTCCATTTGATTCACAATTTTTTTAGTCTCTACTGTGCCTAACTTGTAAGTTAAATTTGATCAGAGGTGT
+GTTCCCAGAGGGGAAAACAGTATATACAGGGTTCAGTACTATCGCATTTCAGGCCTCCACCTGGGTCTTG
+GAATGTGTCCCCCGAGGGGTGATGACTACCTCAGTTGGATCTCCACAGGTCACAGTGACACAAGATAACC
+AAGACACCTCCCAAGGCTACCACAATGGGCCGCCCTCCACGTGCACATGGCCGGAGGAACTGCCATGTCG
+GAGGTGCAAGCACACCTGCGCATCAGAGTCCTTGGTGTGGAGGGAGGGACCAGCGCAGCTTCCAGCCATC
+CACCTGATGAACAGAACCTAGGGAAAGCCCCAGTTCTACTTACACCAGGAAAGGC
+
diff --git a/paper/setup.sh b/paper/setup.sh
@@ -15,18 +15,17 @@
 # wget
 # Perl 5.18+
 # bwa v0.7.14+
-# 
+#
 # Optional software:
 # twoBitToFa
 
-WRK=/path/to/GenoPipe/paper/YKOC-wgs
+WRK=/path/to/GenoPipe/paper
 cd $WRK
 
 module load gcc
 module load bwa
 module load samtools
 
-
 [ -d $WRK/input ] || mkdir $WRK/input
 [ -d $WRK/db ] || mkdir $WRK/db
 
@@ -120,16 +119,33 @@ mv ALL_TAG.fa* ../
 echo "Complete"
 cd $WRK
 
+# Build Human EpiID with HIV genome
+HHIVDB=db/hiv_EpiID
+[ -d $HHIVDB ] || cp -r ../EpitopeID/hg19_EpiID/ $HHIVDB
+if [ ! -f $HHIVDB/FASTA_genome/genome.fa ]; then
+        echo "**Setup Human EpiID genome..."
+        cp input/hg19.fa $HHIVDB/FASTA_genome/genome.fa
+        echo "BWA Indexing genome..."
+        bwa index $HHIVDB/FASTA_genome/genome.fa
+        echo "Complete"
+fi
+echo "Setup HIV genome for Human EpiID..."
+cp input/AF324493.2_HIV-1_vector_pNL4-3.fa $HHIVDB/FASTA_tag/Tag_DB/
+rm $HHIVDB/FASTA_tag/ALL_TAG.fa*
+cd $HHIVDB/FASTA_tag/Tag_DB
+cat *.fa *.fna *.ffn *.fasta > ALL_TAG.fa
+bwa index ALL_TAG.fa
+mv ALL_TAG.fa* ../
+echo "Complete"
+cd $WRK
 
 # Add Yeast Deletion DB to paper/db
 cd $WRK/db
 ln -s ../../DeletionID/sacCer3_Del
 cd $WRK
 
-
 # Add Yeast & Human StrainID DB to paper/db
 cd $WRK/db
 ln -s ../../StrainID/sacCer3_VCF
 ln -s ../../StrainID/hg19_VCF
 cd $WRK
-

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+# logfiles from STDERR and STDOUT of running job files go here`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+# Downloaded FASTQ files and EpitopeID results go here`