├── TEs ├── README.md ├── TE_melp_end.toMap.txt ├── TE_melp_start.toMap.txt ├── TE_melp_end.pan.txt └── TE_melp_start.pan.txt ├── ATAC └── README.md ├── Minimap2_out ├── README.md ├── miniMap_target_end.toMap.txt ├── miniMap_target_start.toMap.txt ├── miniMap_query_end.toMap.txt ├── miniMap_query_start.toMap.txt ├── miniMap_target_end.pan.txt ├── miniMap_target_start.pan.txt ├── miniMap_query_end.pan.txt └── miniMap_query_start.pan.txt ├── sequences └── README.md ├── gene_annotation ├── README.md ├── optix_Hmel2.toMap.txt └── optix_Hmel2.toMap.pan.txt ├── seq-seq-pan_out ├── README.md ├── SeqSeqPan_erato_melp_optix_genomedescription.txt └── SeqSeqPan_erato_melp_optix_consensus.fasta.blockseparated.idx ├── genome_list.txt ├── README.md ├── seq-seq-pan_bedgraph_chrompos.py ├── seq-seq-pan_toFasta.py ├── seq-seq-pan_bedfile_conservation.py ├── seq-seq-pan_blocks_intervals.py └── Plot_minimap_alignment.R /TEs/README.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /ATAC/README.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /Minimap2_out/README.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /sequences/README.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /gene_annotation/README.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /seq-seq-pan_out/README.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /gene_annotation/optix_Hmel2.toMap.txt: -------------------------------------------------------------------------------- 1 | 2 c 2 | 705604 3 | 706407 -------------------------------------------------------------------------------- /genome_list.txt: -------------------------------------------------------------------------------- 1 | sequences/Herato1801_1_2000000.fasta 2 | sequences/Hmel213003_1_2000000.fasta -------------------------------------------------------------------------------- /gene_annotation/optix_Hmel2.toMap.pan.txt: -------------------------------------------------------------------------------- 1 | 2 (source) c 2 | 705604 2126065 3 | 706407 2126871 4 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Genomics tutorial 2 | 3 | Data for [Genomics tutorial](https://stevenvb12.github.io/). 4 | 5 | Web page [tutorial](https://stevenvb12.github.io/). 6 | -------------------------------------------------------------------------------- /seq-seq-pan_out/SeqSeqPan_erato_melp_optix_genomedescription.txt: -------------------------------------------------------------------------------- 1 | 1 Herato1801 dna:scaffold scaffold:v1:Herato1801:1:2000000:1 2000000 2 | 2 Hmel218003 dna:scaffold scaffold:Hmel2:Hmel218003:1:1895173:1 1895173 3 | -------------------------------------------------------------------------------- /seq-seq-pan_out/SeqSeqPan_erato_melp_optix_consensus.fasta.blockseparated.idx: -------------------------------------------------------------------------------- 1 | #Fasta SeqSeqPan_erato_melp_optix_consensus.fasta 2 | #XMFA SeqSeqPan_erato_melp_optix_joined.xmfa 3 | 0;1839;91504;162057;176366;665391;739100;748514;832798;869727;902072;907265;914236;915584;926195;953970;1812466;1817112;1821523;1824328;1826143;2580093;2581180;2582198;2584092;2585437;2734783;2739707;2740974;2745594;3111835;3113145;3114548;3116095;3117495;3118537;3119985;3129279;3139448;3148349;3150709;3162874 -------------------------------------------------------------------------------- /seq-seq-pan_bedgraph_chrompos.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from __future__ import division 4 | import argparse, re 5 | 6 | parser = argparse.ArgumentParser() 7 | parser.add_argument("-I", "--infile", help="bedgraph file", required = True) 8 | parser.add_argument("-g", "--genomeN", help="genome number", required = True) 9 | parser.add_argument("-p", "--scafgenomepos", help="table with genome positions of scaffolds", required = True) 10 | parser.add_argument("-o", "--outfile", help="Output txt file name", action = "store") 11 | args = parser.parse_args() 12 | 13 | infile = args.infile 14 | outfile = args.outfile 15 | genomeNumber = args.genomeN 16 | scafpos = args.scafgenomepos 17 | 18 | s= open(outfile + '_start.txt',"a+") 19 | s.write("\t".join((genomeNumber,"c","\n"))) 20 | 21 | e= open(outfile + '_end.txt',"a+") 22 | e.write("\t".join((genomeNumber,"c","\n"))) 23 | 24 | posIn = open(scafpos, "r") 25 | posLine = posIn.readline() 26 | 27 | posDic = {} 28 | while posLine: 29 | 30 | lineElem = posLine.split('\t') 31 | posDic[lineElem[0]] = lineElem[2] 32 | posLine = posIn.readline() 33 | 34 | 35 | fileIn = open(infile, "r") 36 | fileLine = fileIn.readline() 37 | 38 | n = 1 39 | while fileLine: 40 | 41 | lineElem = fileLine.split('\t') 42 | 43 | if(n ==1): 44 | start = int(lineElem[1]) + int(posDic[lineElem[0]]) + 1 45 | else: 46 | start = int(lineElem[1]) + int(posDic[lineElem[0]]) 47 | 48 | end = int(lineElem[2]) + int(posDic[lineElem[0]]) 49 | 50 | s.write("".join((str(start),"\n"))) 51 | e.write("".join((str(end),"\n"))) 52 | 53 | fileLine = fileIn.readline() 54 | 55 | n+=1 56 | -------------------------------------------------------------------------------- /seq-seq-pan_toFasta.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from __future__ import division 4 | from Bio.Seq import Seq 5 | import argparse, re 6 | 7 | parser = argparse.ArgumentParser() 8 | parser.add_argument("-I", "--infile", help="extract regions from seq-seq-pan", required = True) 9 | parser.add_argument("-g", "--genomeList", help="comma seperated list of genomes in order of seq-seq-pan", required = True) 10 | args = parser.parse_args() 11 | 12 | infile = args.infile 13 | genomes = args.genomeList.split(",") 14 | 15 | 16 | count = 0 17 | 18 | for genome in genomes: 19 | 20 | identified = 0 21 | sequence = str() 22 | 23 | f= open('genome_' + genome + '.fasta',"a+") 24 | #f.write("\t".join(("start","end","\n"))) 25 | count +=1 26 | fileIn = open(infile, "r") 27 | fileLine = fileIn.readline() 28 | fileLine = fileLine.strip() 29 | 30 | print('searching genome ' + str(count) + ' ' + str(genome)) 31 | 32 | while fileLine: 33 | 34 | if '> ' + str(genome) + ':' in fileLine: 35 | 36 | identified += 1 37 | 38 | fileLine = fileIn.readline() 39 | fileLine = fileLine.strip() 40 | #seq = Seq(fileLine) 41 | 42 | sequence = sequence + fileLine 43 | 44 | if '=' not in fileLine and '>' not in fileLine: 45 | lenSeq = len(fileLine) 46 | 47 | if '=' in fileLine and identified == 0: 48 | sequence = sequence + '-' * lenSeq 49 | 50 | if '=' in fileLine and identified == 1: 51 | identified = 0 52 | 53 | fileLine = fileIn.readline() 54 | fileLine = fileLine.strip() 55 | 56 | print('total length: ' + str(len(sequence))) 57 | 58 | f.write("".join((">genome_"+str(genome),"\n"))) 59 | f.write("".join((sequence,"\n"))) 60 | 61 | sequence = str() 62 | 63 | 64 | -------------------------------------------------------------------------------- /seq-seq-pan_bedfile_conservation.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from __future__ import division 4 | from Bio import SeqIO 5 | import argparse, re 6 | 7 | parser = argparse.ArgumentParser() 8 | parser.add_argument("-I", "--infile", help="fasta", required = True) 9 | parser.add_argument("-o", "--outfile", help="txt", required = True) 10 | parser.add_argument("-g", "--genomeList", help="comma seperated list of genomes in order of seq-seq-pan", required = True) 11 | parser.add_argument("-b", "--bedfile", help="bedfile of intersect", required = True) 12 | args = parser.parse_args() 13 | 14 | infile = args.infile 15 | outfile = args.outfile 16 | bedfile = args.bedfile 17 | genomes = args.genomeList.split(",") 18 | 19 | bedfile = open(bedfile, "r") 20 | 21 | records = list(SeqIO.parse(infile, "fasta")) 22 | 23 | seq1 = records[0].seq 24 | seq2 = records[1].seq 25 | 26 | #print(seq1) 27 | #print(seq2) 28 | 29 | print(len(seq1)) 30 | print(len(seq2)) 31 | 32 | bedLine = bedfile.readline() 33 | bedLine = bedLine.strip() 34 | 35 | f = open(outfile + '.txt',"w+") 36 | f.write("\t".join(("start", "end", "length", "IDY", "missing1", "missing2", "\n"))) 37 | 38 | while bedLine: 39 | 40 | bedElem = bedLine.split('\t') 41 | 42 | inter1 = seq1[int(bedElem[1]):int(bedElem[2])] 43 | inter2 = seq2[int(bedElem[1]):int(bedElem[2])] 44 | 45 | if(int(bedElem[1]) == int(bedElem[2])): continue 46 | 47 | score = 0 48 | inter1_N = 0 49 | inter2_N = 0 50 | 51 | 52 | for i in range(0,len(inter1)): 53 | 54 | inter1_base = inter1[i] 55 | inter2_base = inter2[i] 56 | 57 | if inter1_base == inter2_base: 58 | score = score + 1 59 | if inter1_base == '-': 60 | inter1_N = inter1_N + 1 61 | if inter2_base == '-': 62 | inter2_N = inter2_N + 1 63 | 64 | f.write("\t".join((bedElem[1], 65 | bedElem[2], 66 | str(len(inter1)), 67 | str(round(score/len(inter1),4)), 68 | str(round(inter1_N/len(inter1),4)), 69 | str(round(inter2_N/len(inter1),4)),"\n"))) 70 | 71 | 72 | bedLine = bedfile.readline() 73 | bedLine = bedLine.strip() 74 | 75 | 76 | -------------------------------------------------------------------------------- /seq-seq-pan_blocks_intervals.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | # Use as: python seq-seq-pan_blocks_intervals.py -I SeqSeqPan_erato_melp_noNewline.xmfa -g 1,2 4 | 5 | from __future__ import division 6 | from Bio.Seq import Seq 7 | import argparse, re 8 | 9 | parser = argparse.ArgumentParser() 10 | parser.add_argument("-I", "--infile", help="xmfa file with no newlines from seq-seq-pan", required = True) 11 | parser.add_argument("-g", "--genomeList", help="comma separated list of genomes in order of seq-seq-pan genome", required = True) 12 | args = parser.parse_args() 13 | 14 | infile = args.infile 15 | genomes = args.genomeList.split(",") 16 | 17 | count = 0 18 | 19 | for genome in genomes: 20 | 21 | identified = 0 22 | sequence = str() 23 | sequenceOr = str() 24 | 25 | f= open(genome + '_blocks_intervals.txt',"w+") 26 | #f.write("\t".join(("start","end","\n"))) 27 | count +=1 28 | fileIn = open(infile, "r") 29 | fileLine = fileIn.readline() 30 | fileLine = fileLine.strip() 31 | 32 | print('searching genome ' + str(count) + ' ' + str(genome)) 33 | 34 | while fileLine: 35 | 36 | if '> ' + str(genome) + ':' in fileLine: 37 | 38 | identified += 1 39 | 40 | fileLine = fileIn.readline() 41 | fileLine = fileLine.strip() 42 | seq = Seq(fileLine) 43 | 44 | sequence = sequence + seq 45 | 46 | if '=' not in fileLine and '>' not in fileLine: 47 | lenSeq = len(fileLine) 48 | 49 | if '=' in fileLine and identified == 0: 50 | sequence = sequence + '-' * lenSeq 51 | 52 | if '=' in fileLine and identified == 1: 53 | identified = 0 54 | 55 | fileLine = fileIn.readline() 56 | fileLine = fileLine.strip() 57 | 58 | print('total length: ' + str(len(sequence))) 59 | start = 0 60 | for i in range(len(sequence)): 61 | 62 | if i > 0 and i < len(sequence)-1: 63 | if sequence[i-1] == '-': 64 | if sequence[i] != '-': 65 | start = i 66 | if sequence[i+1] == '-': 67 | if sequence[i] != '-': 68 | end = i+1 69 | f.write("\t".join(("pan",str(start),str(end),"\n"))) 70 | 71 | if sequence[i-1] != '-' and i == len(sequence)-1: 72 | f.write("\t".join(("pan",str(start),str(i),"\n"))) 73 | 74 | sequence = str() 75 | sequenceOr = str() 76 | -------------------------------------------------------------------------------- /TEs/TE_melp_end.toMap.txt: -------------------------------------------------------------------------------- 1 | 2 c 2 | 4351 3 | 6504 4 | 8155 5 | 8930 6 | 9792 7 | 10381 8 | 13385 9 | 16959 10 | 17008 11 | 17158 12 | 17923 13 | 19009 14 | 19712 15 | 20116 16 | 20781 17 | 20911 18 | 27441 19 | 28403 20 | 29226 21 | 29888 22 | 31740 23 | 32627 24 | 32640 25 | 32655 26 | 33184 27 | 33263 28 | 35802 29 | 36119 30 | 36293 31 | 37924 32 | 39303 33 | 39877 34 | 39889 35 | 40023 36 | 40102 37 | 40111 38 | 41042 39 | 40690 40 | 45492 41 | 44507 42 | 45656 43 | 46358 44 | 46731 45 | 47338 46 | 47634 47 | 47774 48 | 48000 49 | 53235 50 | 53257 51 | 58494 52 | 58553 53 | 61669 54 | 61890 55 | 62111 56 | 64557 57 | 64962 58 | 70697 59 | 71515 60 | 72214 61 | 74739 62 | 75070 63 | 75309 64 | 75382 65 | 76242 66 | 77742 67 | 81038 68 | 85314 69 | 87253 70 | 90342 71 | 91667 72 | 95099 73 | 95536 74 | 96325 75 | 96336 76 | 98070 77 | 99364 78 | 100053 79 | 103608 80 | 106611 81 | 110548 82 | 109089 83 | 111320 84 | 112447 85 | 114600 86 | 116357 87 | 117263 88 | 117855 89 | 118413 90 | 118661 91 | 119762 92 | 124621 93 | 124987 94 | 126158 95 | 127910 96 | 128908 97 | 129032 98 | 129171 99 | 134465 100 | 135779 101 | 135588 102 | 135647 103 | 135966 104 | 137075 105 | 137539 106 | 138817 107 | 139492 108 | 140246 109 | 140850 110 | 141437 111 | 142269 112 | 142741 113 | 143518 114 | 143599 115 | 143881 116 | 148929 117 | 151058 118 | 153427 119 | 159628 120 | 163681 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1516393 1026 | -------------------------------------------------------------------------------- /Plot_minimap_alignment.R: -------------------------------------------------------------------------------- 1 | # install and load necessary libraries 2 | 3 | if (!require("BiocManager", quietly = TRUE)) 4 | install.packages("BiocManager") 5 | 6 | BiocManager::install("rtracklayer") 7 | 8 | library(rtracklayer) 9 | 10 | # 4.1. Set you working directory: 11 | # set you working directory (you can also use the '...' under the 'File' tab on 12 | # the right of Rstudio to navigate to your folder then click 'More' > 'Set as 13 | # working directory') 14 | 15 | setwd("G:/My Drive/Workshop_pan_genomics_12042023") 16 | 17 | # 4.2. Load the Minimap2 output 18 | 19 | miniMap_out <- read.table('Minimap2_out/Minimap_melp_erato.sam', header = FALSE, sep = '\t') 20 | 21 | # set the column names 22 | colnames(miniMap_out) <- c('queryName', 'queryLength', 'queryStart', 'queryEnd', 23 | 'char', 24 | 'targetName', 'targetLength', 'targetStart', 'targetEnd', 25 | 'matchingBases', 'matchLength', 'matchQuality') 26 | 27 | # check the table 28 | head(miniMap_out) 29 | 30 | # 4.3. Plot the first Minimap2 match 31 | 32 | # First define x-axis coordinates. This will help us later define the genomic window (xlim) we want to zoom in on. 33 | start = 0 34 | end = 3000000 35 | 36 | # Plot an empty plot (so we can fill it with rectangles (~genome) and polygons (~alignments)). 37 | # For the y-axis (ylim) coordinates I arbitrarily use c(0,10). 38 | plot(NULL, xlim = c(start, end), ylim = c(0,10), axes=F, ylab = '', xlab = '') 39 | 40 | # Now we can draw two simple rectangles, one will define the genomic interval/sequence of H. melpomene (deepskyblue), the other H. erato (mediumseagreen). 41 | rect(0,8,2000000,9, col = 'deepskyblue', border = NA) 42 | rect(0,1,2000000,2, col = 'mediumseagreen', border = NA) 43 | 44 | # We also know the positions of the optix gene and we can add these with the same rect() function trick. 45 | rect(705604,9.2,706407,10, col = 'red', border = 'red') # position optix melpomene (only has one exon) 46 | 47 | rect(1239943,0,1239972,0.8, col = 'red', border = 'red') # first exon position optix erato 48 | rect(1250591,0,1251211,0.8, col = 'red', border = 'red') # second exon position optix erato 49 | rect(1239943,0.4,1251211,0.4, col = 'red', border = 'red') # A little line between the two and we have a gene model! 50 | 51 | # With the text function, we can add the gene and species names at the appropriate coordinates. 52 | text(706407, 9.6, substitute(paste(italic('optix'))), pos = 4) 53 | text(1251211, 0.4, substitute(paste(italic('optix'))), pos = 4) 54 | 55 | text(start, 7.5, substitute(paste(italic('H. melpomene'))), pos = 4) 56 | text(start, 2.5, substitute(paste(italic('H. erato'))), pos = 4) 57 | 58 | # Finally, with the polygon function, we map the alignment connections between the sequences of H. melpomene (target) and H. erato (query). 59 | polygon(x = c(miniMap_out$targetStart[1], miniMap_out$targetEnd[1], miniMap_out$queryEnd[1], miniMap_out$queryStart[1]), 60 | y = c(8,8,2,2), 61 | col = adjustcolor('black', alpha.f = 0.1), border = FALSE) 62 | ### 63 | 64 | # 4.4. Plot all Minimap2 match 65 | 66 | # First define x-axis coordinates. This will help us later define the genomic window (xlim) we want to zoom in on. 67 | start = 0 68 | end = 3000000 69 | 70 | # Plot an empty plot (so we can fill it with rectangles (~genome) and polygons (~alignments)). 71 | # For the y-axis (ylim) coordinates I arbitrarily use c(0,10). 72 | plot(NULL, xlim = c(start, end), ylim = c(0,10), axes=F, ylab = '', xlab = '') 73 | 74 | # Now we can draw two simple rectangles, one will define the genomic interval/sequence of H. melpomene (deepskyblue), the other H. erato (mediumseagreen). 75 | rect(0,8,2000000,9, col = 'deepskyblue', border = NA) 76 | rect(0,1,2000000,2, col = 'mediumseagreen', border = NA) 77 | 78 | # We also know the positions of the optix gene and we can add these with the same rect() function trick. 79 | rect(705604,9.2,706407,10, col = 'red', border = 'red') # position optix melpomene (only has one exon) 80 | 81 | rect(1239943,0,1239972,0.8, col = 'red', border = 'red') # first exon position optix erato 82 | rect(1250591,0,1251211,0.8, col = 'red', border = 'red') # second exon position optix erato 83 | rect(1239943,0.4,1251211,0.4, col = 'red', border = 'red') # A little line between the two and we have a gene model! 84 | 85 | # With the text function, we can add the gene and species names at the appropriate coordinates. 86 | text(706407, 9.6, substitute(paste(italic('optix'))), pos = 4) 87 | text(1251211, 0.4, substitute(paste(italic('optix'))), pos = 4) 88 | 89 | text(start, 7.5, substitute(paste(italic('H. melpomene'))), pos = 4) 90 | text(start, 2.5, substitute(paste(italic('H. erato'))), pos = 4) 91 | 92 | # Loop through each row in the Minimap2 alignment table and plot each match as a polygon. 93 | for(e in 1:nrow(miniMap_out)){ 94 | 95 | polygon(x = c(miniMap_out$targetStart[e], miniMap_out$targetEnd[e], miniMap_out$queryEnd[e], miniMap_out$queryStart[e]), 96 | y = c(8,8,2,2), 97 | col = adjustcolor('black', alpha.f = 0.1), border = FALSE) 98 | } 99 | ### 100 | 101 | 102 | # 4.5. Modify relative alignment 103 | # Let's make sure optix is aligned in the center of the plot between the two species 104 | 105 | # First define x-axis coordinates. This will help us later define the genomic window (xlim) we want to zoom in on. 106 | start = 0 107 | end = 3000000 108 | 109 | # Calculate the offset between the positions of optix in the two fasta sequences. 110 | # We will use this to modify all the x-axes coordinates for H. melpomene. 111 | plotDiff = 1251211 - 706407 112 | 113 | # Plot an empty plot (so we can fill it with rectangles (~genome) and polygons (~alignments)). 114 | # For the y-axis (ylim) coordinates I arbitrarily use c(0,10). 115 | plot(NULL, xlim = c(start, end), ylim = c(0,10), axes=F, ylab = '', xlab = '') 116 | 117 | # Now we can draw two simple rectangles, one will define the genomic interval/sequence of H. melpomene (deepskyblue), the other H. erato (mediumseagreen). 118 | rect(0+plotDiff,8,2000000+plotDiff,9, col = 'deepskyblue', border = NA) 119 | rect(0,1,2000000,2, col = 'mediumseagreen', border = NA) 120 | 121 | # We also know the positions of the optix gene and we can add these with the same rect() function trick. 122 | rect(705604+plotDiff,9.2,706407+plotDiff,10, col = 'red', border = 'red') # position optix melpomene (only has one exon) 123 | 124 | rect(1239943,0,1239972,0.8, col = 'red', border = 'red') # first exon position optix erato 125 | rect(1250591,0,1251211,0.8, col = 'red', border = 'red') # second exon position optix erato 126 | rect(1239943,0.4,1251211,0.4, col = 'red', border = 'red') # A little line between the two and we have a gene model! 127 | 128 | # With the text function, we can add the gene and species names at the appropriate coordinates. 129 | text(706407+plotDiff, 9.6, substitute(paste(italic('optix'))), pos = 4) 130 | text(1251211, 0.4, substitute(paste(italic('optix'))), pos = 4) 131 | 132 | text(start, 7.5, substitute(paste(italic('H. melpomene'))), pos = 4) 133 | text(start, 2.5, substitute(paste(italic('H. erato'))), pos = 4) 134 | 135 | # Plot the polygons representing the alignments. 136 | for(e in 1:nrow(miniMap_out)){ 137 | 138 | polygon(x = c(miniMap_out$targetStart[e]+plotDiff, miniMap_out$targetEnd[e]+plotDiff, miniMap_out$queryEnd[e], miniMap_out$queryStart[e]), 139 | y = c(8,8,2,2), 140 | col = adjustcolor('black', alpha.f = 0.1), border = FALSE) 141 | } 142 | ### 143 | 144 | 145 | # 4.6. Zoom in 146 | ### 147 | # Exercise: Zoom in on 10,000 bp before and 200,000 bp after optix 148 | 149 | # but before we do this, let's build the layout of our plot first 150 | 151 | layout(matrix(c(1,4,5,3,6,7,2), nrow=7, byrow=TRUE), height = c(0.5,1,1,2,1,1,0.5)) 152 | layout.show(n=7) 153 | 154 | par(mar = c(0.5,5,0.5,1), xpd = FALSE) 155 | 156 | # Define the interval (relative to the H. erato genome) 157 | start = 1239943 - 10000 158 | end = 1251211 + 200000 159 | 160 | # Plot the title of the plot 161 | plot(NULL, xlim=c(start,end), ylim = c(0,1), axes=FALSE, ann=FALSE) 162 | mtext('Minimap2 aligned genome plot', side = 1, cex=1, col = 'black', line =-1) 163 | 164 | # Plot the x-axis as a separate plot 165 | plot(NULL, xlim=c(start,end), ylim = c(0,1), axes=FALSE, ann=FALSE) 166 | axis(1, at = seq(0,3124353, by=10000), labels = NA, line =-3) 167 | axis(1, at = seq(0,3124353, by=100000), labels = round(seq(0/1000000,3124353/1000000, by=0.1),1), line =-3) 168 | mtext('Chromosome position', side = 1, cex=0.8, col = 'black', line =-1) 169 | 170 | # Calculate the offset between the positions of optix in the two fasta sequences. 171 | # We will use this to modify all the x-axes coordinates for H. melpomene. 172 | plotDiff = 1251211 - 706407 173 | 174 | # Plot an empty plot (so we can fill it with rectangles (~genome) and polygons (~alignments)). 175 | # For the y-axis (ylim) coordinates I arbitrarily use c(0,10). 176 | plot(NULL, xlim = c(start, end), ylim = c(0,10), axes=F, ylab = '', xlab = '') 177 | 178 | # Now we can draw two simple rectangles, one will define the genomic interval/sequence of H. melpomene (deepskyblue), the other H. erato (mediumseagreen). 179 | rect(0+plotDiff,8,2000000+plotDiff,8.8, col = 'deepskyblue', border = NA) 180 | rect(0,1.2,2000000,2, col = 'mediumseagreen', border = NA) 181 | 182 | # We also know the positions of the optix gene and we can add these with the same rect() function trick. 183 | rect(705604+plotDiff,9.2,706407+plotDiff,10, col = 'red', border = 'red') # position optix melpomene (only has one exon) 184 | 185 | rect(1239943,0,1239972,0.8, col = 'red', border = 'red') # first exon position optix erato 186 | rect(1250591,0,1251211,0.8, col = 'red', border = 'red') # second exon position optix erato 187 | rect(1239943,0.4,1251211,0.4, col = 'red', border = 'red') # A little line between the two and we have a gene model! 188 | 189 | # With the text function, we can add the gene and species names at the appropriate coordinates. 190 | text(706407+plotDiff, 9.6, substitute(paste(italic('optix'))), pos = 4) 191 | text(1251211, 0.4, substitute(paste(italic('optix'))), pos = 4) 192 | 193 | text(start, 7.5, substitute(paste(italic('H. melpomene'))), pos = 4) 194 | text(start, 2.5, substitute(paste(italic('H. erato'))), pos = 4) 195 | 196 | for(e in 1:nrow(miniMap_out)){ 197 | 198 | # I add here a filter so that alignments outside of the plotting area don't get included. 199 | if(miniMap_out$targetStart[e]+plotDiff > start & miniMap_out$targetEnd[e]+plotDiff < end & miniMap_out$queryStart[e] > start & miniMap_out$queryEnd[e] < end){ 200 | 201 | polygon(x = c(miniMap_out$targetStart[e]+plotDiff, miniMap_out$targetEnd[e]+plotDiff, miniMap_out$queryEnd[e], miniMap_out$queryStart[e]), 202 | y = c(8,8,2,2), 203 | col = adjustcolor('black', alpha.f = miniMap_out$matchingBases[e]/miniMap_out$matchLength[e]), border = FALSE) 204 | 205 | } 206 | } 207 | 208 | mtext('Minimap2 alignment', side = 2, cex=0.8, padj = -1, col = 'black') 209 | ### 210 | 211 | 212 | 213 | # 4.7. Add transposable element annotations 214 | # We can plot Transposable Elements on top of this 215 | 216 | # Load the TE tables (only the columns that are relevant to us). 217 | TE_erato <- read.table('TEs/H_erato_1801_TE.txt', header = FALSE)[,c(2,5:7)] 218 | TE_melp <- read.table('TEs/H_melp_18003_TE.txt', header = FALSE)[,c(2,5:7)] 219 | 220 | # Fix the column names 221 | colnames(TE_erato) <- c('subs','scaf', 'start', 'end') 222 | colnames(TE_melp) <- c('subs','scaf', 'start', 'end') 223 | 224 | # (optional) remove TEs with large number of substitutions compared to database 225 | TE_erato <- subset(TE_erato, TE_erato$subs < 15) 226 | TE_melp <- subset(TE_melp, TE_melp$subs < 15) 227 | 228 | # Loop through the rows and plot each TE as a small orange rectangle. 229 | 230 | for(e in 1:nrow(TE_melp)){ 231 | rect(TE_melp$start[e]+plotDiff,8.8,TE_melp$end[e]+plotDiff,9, col = 'orange', border = NA) 232 | } 233 | 234 | for(e in 1:nrow(TE_erato)){ 235 | rect(TE_erato$start[e],1,TE_erato$end[e],1.2, col = 'orange', border = NA) 236 | } 237 | 238 | # Add a little text note on the plot 239 | mtext('TE', side = 1, cex=0.8, padj = -3, las = 1, adj=1, col = 'orange') 240 | 241 | 242 | # 4.8. Add ATAC-seq data tracks 243 | # Add the ATAC-seq data of some butterfly brain and wing tissue 244 | 245 | # Load the ATAC-seq data (make sure the 'rtracklayer' is loaded). 246 | 247 | erato_5th_brain <- import.bedGraph("ATAC/brain_5th_H_erato_normalized_mean.w30s0bin.bg") 248 | erato_5th_FW <- import.bedGraph("ATAC/FW_5th_H_erato_normalized_mean.w30s0bin.bg") 249 | 250 | melp_5th_brain <- import.bedGraph("ATAC/brain_5th_H_melp_normalized_mean.w30s0bin.bg") 251 | melp_5th_FW <- import.bedGraph("ATAC/FW_5th_H_melp_normalized_mean.w30s0bin.bg") 252 | 253 | # Sample 1 254 | 255 | # Plot an empty plot (remember, this will fill a panel defined by the layout function). 256 | plot(NULL, xlim=c(start,end), ylim = c(0,200), axes=FALSE, ann=FALSE) 257 | # Tell R the next plot call will be to the one that is already there and not initiate a new one. 258 | par(new = TRUE) 259 | # Plot the ATAC-seq track. 260 | plot(0.5*(start(melp_5th_brain) + end(melp_5th_brain))+plotDiff, melp_5th_brain$score, type='l', xlim = c(start,end), ylim = c(0,200), ylab = "", yaxt = "n", lwd = 1, xlab = "", xaxt = "n", main = "", bty='none', col = "black") 261 | 262 | # Add some text specifying the stage and tissue of the sample. 263 | mtext('ATAC-seq 5th instar brain', side = 1, cex=0.8, padj = 0, las = 1, adj=1) 264 | # Add the y-axis labels 265 | axis(2, at = seq(0,200, by=50), line = 1) 266 | mtext('Score', side = 2, cex=0.8, line = 3) 267 | 268 | # Sample 2 269 | 270 | plot(NULL, xlim=c(start,end), ylim = c(0,200), axes=FALSE, ann=FALSE) 271 | par(new = TRUE) 272 | plot(0.5*(start(melp_5th_FW) + end(melp_5th_FW))+plotDiff, melp_5th_FW$score, type='l', xlim = c(start,end), ylim = c(0,200), ylab = "", yaxt = "n", lwd = 1, xlab = "", xaxt = "n", main = "", bty='none', col = "black") 273 | 274 | mtext('ATAC-seq 5th instar FW', side = 1, cex=0.8, padj = 0, las = 1, adj=1) 275 | axis(2, at = seq(0,200, by=50), line = 1) 276 | mtext('Score', side = 2, cex=0.8, line = 3) 277 | 278 | # Sample 3 279 | 280 | plot(NULL, xlim=c(start,end), ylim = c(0,200), axes=FALSE, ann=FALSE) 281 | par(new = TRUE) 282 | plot(0.5*(start(erato_5th_brain) + end(erato_5th_brain)), erato_5th_brain$score, type='l', xlim = c(start,end), ylim = c(0,200), ylab = "", yaxt = "n", lwd = 1, xlab = "", xaxt = "n", main = "", bty='none', col = "black") 283 | 284 | mtext('ATAC-seq 5th instar brain', side = 1, cex=0.8, padj = 0, las = 1, adj=1) 285 | axis(2, at = seq(0,200, by=50), line = 1) 286 | mtext('Score', side = 2, cex=0.8, line = 3) 287 | 288 | # Sample 4 289 | 290 | plot(NULL, xlim=c(start,end), ylim = c(0,200), axes=FALSE, ann=FALSE) 291 | par(new = TRUE) 292 | plot(0.5*(start(erato_5th_FW) + end(erato_5th_FW)), erato_5th_FW$score, type='l', xlim = c(start,end), ylim = c(0,200), ylab = "", yaxt = "n", lwd = 1, xlab = "", xaxt = "n", main = "", bty='none', col = "black") 293 | 294 | mtext('ATAC-seq 5th instar FW', side = 1, cex=0.8, padj = 0, las = 1, adj=1) 295 | axis(2, at = seq(0,200, by=50), line = 1) 296 | mtext('Score', side = 2, cex=0.8, line = 3) 297 | -------------------------------------------------------------------------------- /Minimap2_out/miniMap_target_end.pan.txt: -------------------------------------------------------------------------------- 1 | 2 (source) c 2 | 1223 939895 3 | 5751 944977 4 | 6882 946125 5 | 7651 949514 6 | 7805 949668 7 | 8097 949960 8 | 8717 950585 9 | 9213 951674 10 | 12035 956929 11 | 14696 962932 12 | 15619 964559 13 | 16547 966408 14 | 20195 973125 15 | 21161 977629 16 | 23059 983374 17 | 24618 985699 18 | 25529 987950 19 | 25974 990300 20 | 27368 993319 21 | 28829 995409 22 | 30855 999409 23 | 31528 1001095 24 | 35250 1009141 25 | 37219 1011340 26 | 41244 1017356 27 | 45922 1026817 28 | 46595 1027773 29 | 47326 1028504 30 | 48691 1030384 31 | 49287 1032532 32 | 49552 1033333 33 | 50891 1035217 34 | 51634 1036373 35 | 52539 1038329 36 | 54133 1042212 37 | 54692 1044494 38 | 55319 1046290 39 | 58542 1051333 40 | 62054 1056415 41 | 63204 1057875 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