GenomeJack Browser Appendix
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1 GenomeJack Browser Appendix 3.1 MITSUBISHI SPACE SOFTWARE CO., LTD
2 Contents BED BED Graph TSV (TXT) CSV GFF GTF SAM / BAM VCF WIG / BigWig TSV Tutorials RNA-seq TopHat Cufflinks GenomeJack Chip-seq Bowtie MACS ChIP-seq GenomeJack GenomeJack Web Start Web Start i
3 CHAPTER BED BED BED : 1. chrom 2. chromstart 3. chromend 9 : 1. name 2. score 3. shade 4. scoreinrange 5. strand 6. thickstart 7. thickend 8. itemrgb 1
4 9. blockcount 10. blocksizes 11. blockstarts ) chr No. chr.start chr.end name chr chr chr BED 2
5 1.2 BED Graph BED Graph probability scores transcriptome data BED Graph BED format track definition line track definition line track type=bedgraph Start End Start 1base name tracklabel User Track description centerlabel User Supplied Track visibility full dense hide hide color RRR,GGG,BBB 255,255,255 altcolor RRR,GGG,BBB 128,128,128 priority N 100 autoscale on off on alwayszero on off off griddefault on off off maxheightpixels max:default:min 128:128:11 graphtype bar points bar viewlimits lower:upper ylinemark real-value 0.0 ylineonoff on off off windowingfunction maximum mean minimum maximum smoothingwindow off [2-16] off ) track type=bedgraph name="bedgraph Format" description="bedgraph format" visibility=full color=200,100,0 altcolor=0,100,200 priority=20 hs_ch hs_ch hs_ch hs_ch hs_ch hs_ch hs_ch hs_ch hs_ch BED Graph 3
6 1.3 TSV (TXT) TSV (tab-separated values) TSV (TXT) 4
7 1.4 CSV CSV (comma-separated values) (, ) 100 ) #chr,start,end,data1,data2 chr1,1,100,test1,test2 chr1,101,200,test1,"test2_1,test2_2" 1.4. CSV 5
8 1.5 GFF GFF (General Feature Format) GFF standard file format GFF 9 1. seqname sccafold 2. source feature 3. feature ferture CDS, start_codon, stop_codon, exon 4. start feature 5. end feature. 6. score strand frame feature coding exon frame 0-2 coding exon. 9. group ) track name=regulatory description="telegene(tm) Regulatory Regions" chr11 TeleGene enhancer touch1 chr11 TeleGene promoter touch1 chr11 TeleGene promoter touch GFF 6
9 1.6 GTF GTF GFF GTF GFF GTF group GFF gene_id transcript_id exon number type(ex. gene_id) value(ex. AB ) ; gene_id transcript_id 1. seqname 2. source 3. feature CDS exon strat codon stop codon. 4. start 5. end DATA. 6. score 0~1000 track line usescore 1 DATA ( ) 7. strand + +, -, 8. frame feature CDS 0~2 ORF. 9. group 1.6. GTF 7
10 gene_id value geneid transcript_id value transcriptid ) chr1 Cufflinks exon gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM " "; frac " "; conf_lo " "; conf_hi " "; cov " "; chr1 Cufflinks transcript gene_id "CUFF.423"; transcript_id "CUFF.423.1"; FPKM " "; frac " "; conf_lo " "; conf_hi " "; cov " "; chr1 Cufflinks exon gene_id "CUFF.423"; transcript_id "CUFF.423.1"; exon_number "1"; FPKM " "; frac " "; conf_lo " "; conf_hi " "; cov " "; chr1 Cufflinks transcript gene_id "CUFF.425"; transcript_id "CUFF.425.1"; FPKM " "; frac " "; conf_lo " "; conf_hi " "; cov " "; chr1 Cufflinks exon gene_id "CUFF.425"; transcript_id "CUFF.425.1"; exon_number "1"; FPKM " "; frac " "; conf_lo " "; conf_hi " "; cov " "; 1.6. GTF 8
11 1.7 SAM / BAM SAM NGS SAM SAMtools SAM SAM BAM SAM SAMtools SAM ) VN:1.0 SN:hs_ch01 ID:TopHat VN:1.3.0 CL:/home/hoge/tophat/tophat -o./fuga /home/hoge/bowtie/indexes/hg19 hoge.fastq : HWI-ST256_0153_A81NGJABXX:6:44:1779:132415#0 16 chr M * 0 0 ACAAGTAGGAAAAGTAACTCAGAACAAGGGCAAAGGTCAACTCTGCT CAGCTCTTCCAAAGGTCATGCAAAGGTCATTCAAAGGTCATTCAAAGGTCATT bbedegggg bgggfggdgefffffeccdbcgeeegccbbagbgggdggggfgggeegggggggggggggggg gggggggfgggggggggfgggggggggg NM:i:0 NH:i:1 HWI-ST256_0153_A81NGJABXX:6:41:20727:81915#0 16 chr M * 0 0 GATTGATGGTTTGAGCTGTATAACCCAGTCCCATCTCTCTGGTTATGT CAGATTCAGTCACATGTCCCAAGCTCT bddgeee^ba[dbgbfeaefdf_eefffdfdda adbb^effefeefeffeegggfffffcefefeggegffgeeg NM:i:0 NH:i: SAM / BAM 9
12 HWI-ST256_0153_A81NGJABXX:6:24:2715:19715#0 16 chr M * 0 0 CGGCAGCCACAGTCAAGTAGCGCCCATGTCTTGGA a ddeedfe ^]UWV abaa^ax]vy[[z]y[ NM:i:0 NH:i:3 CC:Z:chr2 CP:i: HI:i:0 HWI-ST256_0153_A81NGJABXX:6:62:8552:153328#0 16 chr M * 0 0 TCTGTTTGGCGTAAGCAGATTGAGCTAGTTATAATTATTCCTCATAGG GAGAGAAGGATGAAGGGGTATGCTATATATTTTGTTAGTGGGTCTAGAATAA dfddfggg^ ggggggagggffegbgggeeeeegegead eaageeggggeaggggeggggdc]^a[xbabgg gggggggfgggggggggggggggggggg NM:i:0 NH:i:2 CC:Z:chrM CP:i:10909 HI:i:0 HWI-ST256_0153_A81NGJABXX:6:48:17219:11563#0 16 chr M * 0 0 TAAGCAGATTGAGCTAGTTATAATTATTCCTCATAGGGAGAGAAGGAT GAAGGGGTATGCTATATATTTTGTTAGTGGGTCTAGAATAATGGAGATGCGA eedeefdf egafg_dccgc_deddcg]ggcfgfgggggfgfgggddddd_nyvu[dcyeagggggg gfgg gggfeffddddddeyfffdedffdebee NM:i:0 NH:i:2 CC:Z:chrM CP:i:10898 HI:i:0 HWI-ST256_0153_A81NGJABXX:6:26:8890:148254#0 272 chr M * 0 0 TACAATTATTCCTCATAGGGAGAGAAGGATGAA a Tfffefgggg_ gggggggggffggggggfeg NM:i:1 NH:i:2 CC:Z:chrM CP:i:10947 HI:i: 1.7. SAM / BAM 10
13 1.8 VCF Variant Call Format (VCF) single nucleotide variants insertions/deletions, copy number variants and structural variants VCF meta-information lines data lines ) ##fileformat=vcfv4.1 ##filedate= ##source=myimputationprogramv3.1 ##reference=file:///seq/references/1000genomespilot-ncbi36.fasta ##contig=<id=20,length= ,assembly=b36,species="homo sapiens"> ##phasing=partial ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP,build 129"> ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> ##FILTER=<ID=q10,Description="Quality below 10"> ##FILTER=<ID=s50,Description="Less than 50% of samples have data"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA rs G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0 0:48:1:51,51 1 0:48:8:51,51 1/1:43:5:., T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0 0:49:3:58,50 0 1:3:5:65,3 0/0:41: rs A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1 2:21:6:23,27 2 1:2:0:18,2 2/2:35: T. 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0 0:54:7:56,60 0 0:48:4:51,51 0/0:61: microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40: VCF 11
14 1.9 WIG / BigWig WIG GC probability scores WIG BedGraph WIG variablestep fixedstep WIG 1 track definition line WIG declaration line 2 BigWig WIG wigtobigwig WIG Wig variablestep variablestep chrom=chrn [span=windowsize] chromstarta datavaluea chromstartb datavalueb... etc etc... ) variablestep chrom=chr fixedstep fixedstep chrom=chrn start=position step=stepinterval [span=windowsize] datavalue1 datavalue2... etc WIG / BigWig 12
15 ) fixedstep chrom=chr3 start= step= ,22,33 chr , , span WIG / BigWig 13
16 CHAPTER 2 TSV 2.1 TSV GenomeJack TSV GenomeJack TSV 1. (Mac OS X control + ) [Import] > [TSV] 2. 14
17 3. Setup Input / Output Resources Next 4. Set Parameters / Execute Create : Setting/Setting 5. Header Setting / File Import Setting 2.1. TSV 15
18 0 Next : Determine Regions / File Import Setting F1 F2 F3 By Three Columns 2.1. TSV 16
19 : By One Column : 1 By Three Columns : 7. Column Settings / File Import Settings Finish Use As Label Create Index 2.1. TSV 17
20 8. Select 9. Import Setting OK TSV 2.1. TSV 18
![10. [View] > [Show Table View] >](/docs-images/84/90818422/images/21-1.jpg "[ ] TSV 11. 12. Edit 2.1. TSV 19")
21 10. [View] > [Show Table View] > [ ] TSV Edit 2.1. TSV 19
22 OK TSV 20
23 14. CSV TSV 21
24 2.2 GenomeJack 1. (Mac OS X control + ) [Import] > [arrayprobe] Setup Input / Output Resources Next
25 4. Set Parameters / Execute Create 5. 1 Next
26 6. Determine Regions / File Import Setting Name By One Column
27 : By One Column : 1 By Three Columns : 7. Column Settings / File Import Setting ID ID Create ndex on Finish
28 : Use As Label ID Use As Label Create ndex 8. Select
29 9. Import Setting OK (Mac OS X control + ) [Import] > [array]
30 Setup Input / Output Resources Next 14. Set Parameters / Execute _D_DNABack_BCLeft_ txt Select Probe Import Setting Create
31 15. Header Setting / Import Array Data Settings 15 Next 16. Determine Probe Position / Import Array Data Settings ID ID ID Doping Control Name Next
32 17. Column Number / Import Array Data Settings
33 : 18. Column Setting / Import Array Data Settings Finish
34 19. Import Setting OK
35
36 CHAPTER 3 Tutorials Fastq GenomeJack Browser RNA-Seq Chip-Seq RNA-seq RNA-seq Paired-end FASTQ SRR SRR MCF-7 breast cancer cell line RNA-seq cdna RNA-seq GenomeJack hg TopHat 3. Cufflinks 34
37 4. GenomeJack TopHat Cufflinks TopHat Bowtie2 TopHat Cufflinks Bowtie2 TopHat Transcriptome Cufflinks tophat linux_x86_64.tar.gz Bowtie2 cufflinks linux_x86_64.tar.gz TopHat bowtie2/2.1.0/bowtie linux-x86_64.zip/download Bowtie bowtie indexes indexes hg19.zip ftp://ftp.cbcb.umd.edu/pub/data/bowtie2_indexes/hg19.zip : PATH 3.1. RNA-seq 35
38 3.1.2 TopHat 1. SRR064286_1.fastq SRR064286_2.fastq human genome tophat2 -r library-type fr-unstranded -o./srr064286_tophat_out path/to/bowtie_index SRR064286_1.fastq SRR064286_2.fastq -o SRR064286_out 2. SRR tophat2 -r library-type fr-unstranded -o./srr064437_tophat_out path/to/bowtie_index SRR064437_1.fastq SRR064437_2.fastq accepted_hits.bam Cufflinks 1. cufflinks -o./srr064437_cufflinks_out -G refgene.gtf --library-type fr-unstranded SRR064437_tophat_out/accepted_hits.bam cufflinks -o./srr064286_cufflinks_out -G refgene.gtf --library-type fr-unstranded SRR064286_tophat_out/accepted_hits.bam refgene.gtf RefSeq URL RNA-seq 36
39 human RefSeq Genes GTF transcripts.gtf GenomeJack transcripts.gtf GenomeJack FPKM KREMEN2 MCF RNA-seq 37
40 3.2 Chip-seq ChIP-seq SRR SRR HeLa PHF8 ChIP-seq HeLa IgG ChIP-seq (Control) GenomeJack hg19 : PHF8 H3K4me Bowtie 3. SAMtools 4. MACS ChIP-seq 5. GenomeJack Bowtie2 SAMtools MACS Bowtie SAMtools MACS Bowtie2 SAMtools RNA-seq Bowtie MAC 3.2. Chip-seq 38
41 MACS showfiles.php?group_id= Bowtie ChIPseq : PATH Bowtie 1. SRR fastq SRR fastq human genome bowtie2 -x path/to/hg19 -U SRR fastq -S SRR sam SAM 2. SRR fastq bowtie2 -x path/to/hg19 -U SRR fastq -S SRR sam 3. SAMtools SAM BAM GenomeJack BAM samtools view -bhs -o SRR bam SRR sam samtools sort SRR bam SRR sorted samtools index SRR sorted.bam samtools view -bhs -o SRR bam SRR sam samtools sort SRR bam SRR sorted samtools index SRR sorted.bam : view : SAM BAM sort : BAM 3.2. Chip-seq 39
42 index : BAM MACS ChIP-seq 1. SRR control SRR macs2 -t SRR sorted.bam -c SRR sorted.bam -f BAM -n SRP g hs SRP010008_peaks.bed SRP010008_summits.bed SRP010008_MACS_wiggle/treat/ wig.gz GenomeJack 1. SRP010008_peaks.xls GenomeJack PEX10 PHF8 ChIP-seq PEX10 PHF Chip-seq 40
43 CHAPTER 4 GenomeJack GenomeJack Web Start Web Start Web Start GenomeJack 4.1 Web Start GenomeJack Web Start Web Start 1. GenomeJACK 41
44 gj lib settings temp GenomeJack GenomeJack GenomeJack GenomeJack 2. gj Web Start ( GenomeJACK3.0 ) 3. gj genomejack.ini "sessionfilepath": " /gj/genomejack.session" "sessionfilepath": "Web Start /gj/genomejack.session" 4. Web Start GenomeJack Web Start 4.1. Web Start 42
45 4.2 Web Start GenomeJack Web Start Web Start 1. Web Start ( GenomeJACK3.0) gj settings temp GenomeJack GenomeJack 2. Web Start gj GenomeJACK 3. gj genomejack.ini "sessionfilepath": "Web Start /gj/genomejack.session" "sessionfilepath": " /gj/genomejack.session" 4. GenomeJack Web Start 4.2. Web Start 43
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