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Galaxy History ' Histones chr1'


DatasetAnnotation
1: H3K27me3_chr1.sorted.noDup.bam
256.9 Mb
format: bam, database: hg19
Info: uploaded bam file
Binary bam alignments file
2: Input_for_H3K27me3_chr1.sorted.noDup.bam
283.9 Mb
format: bam, database: hg19
Info: uploaded bam file
Binary bam alignments file
3: FastQC on data 1
11.0 Kb
format: html, database: hg19
HTML file
4: flagstat on data 2
11 lines
format: txt, database: hg19
8627850 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
8627850 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
5: Bam to Bai on data 1
5,181 lines
format: bai, database: hg19
binary file
6: Bam to Bai on data 2
5,637 lines
format: bai, database: hg19
binary file
11: MACS on data 2 and data 1 (peaks: bed)
20,842 regions
format: bed, database: hg19
1.Chrom2.Start3.End4.Name5
chr1229013229308MACS_peak_136.10
chr1796955799282MACS_peak_284.51
chr1799855800589MACS_peak_349.21
chr1801063801738MACS_peak_462.07
chr1804128804668MACS_peak_540.02
chr1805547808175MACS_peak_632.83
12: MACS on data 2 and data 1 (treatment: wig)
~11,000,000 lines
format: wig, database: hg19
12
track type=wiggle_0 name="MACS_in_Galaxy_treat_chr1" description="Extended tag pileup from MACS version 1.4.2 20120305 for every 20 bp"
variableStep chrom=chr1 span=20
134411
134611
134812
135012
13: MACS on data 2 and data 1 (control: wig)
~12,000,000 lines
format: wig, database: hg19
12
track type=wiggle_0 name="MACS_in_Galaxy_control_chr1" description="Extended tag pileup from MACS version 1.4.2 20120305 for every 20 bp"
variableStep chrom=chr1 span=20
132013
132215
132417
132618
14: MACS on data 2 and data 1 (html report)
4.8 Kb
format: html, database: hg19
HTML file
15: Wig-to-bigWig on data 13
34.7 Mb
format: bigwig, database: hg19
display at UCSC main
Binary UCSC BigWig file
17: H3K27me3_chr1.sorted.noDup.bam (as BED)
~8,500,000 regions
format: bed, database: hg19
1.Chrom2.Start3.End4.Name56.Strand
chr11343413509171_989_1931_F3255+
chr11346213537361_1840_1570_F3255+
chr1149071498273_817_490_F3255-
chr11617516250210_1237_1143_F3255+
chr11622116296656_251_277_F3255+
chr1162861636152_1593_1996_F3255-
40: Wig-to-bigWig on data 12
32.3 Mb
format: bigwig, database: hg19
display at UCSC main
Binary UCSC BigWig file
45: Input_for_H3K27me3_chr1.sorted.noDup.bam (as BED)
~9,300,000 regions
format: bed, database: hg19
1.Chrom2.Start3.End4.Name56.Strand
chr11326213337263_266_1082_F3255-
chr11326513340224_728_1895_F3255+
chr11327113346438_1626_1731_F3255-
chr113272133479_1874_718_F3255-
chr11329113366151_1175_849_F3255-
chr1132931336889_1297_900_F3255-
61: CCAT on data 45 and data 17 (peaks)
61,478 regions
format: interval, database: hg19
1.Chrom23.Start4.End5678
chr115323552515323395015324485096149.1957310.043000
chr124599475245936502460995090148.6110530.043000
chr1250572525025002507550109218.3959060.043000
chr113835125138284501383955073108.0389860.043000
chr11195288751195113001195302507097.9825340.043000
chr123055172523054055023056130074107.9559630.043000
62: CCAT on data 45 and data 17 (regions)
25,206 regions
format: interval, database: hg19
1.Chrom23.Start4.End5678
chr115323552515323395015324485096149.1957310.043000
chr124599475245936502460995090148.6110530.043000
chr1250572525025002507550109218.3959060.043000
chr113835125138284501383955073108.0389860.043000
chr11195288751195113001195302507097.9825340.043000
chr123055172523054055023056130074107.9559630.043000
63: CCAT on data 45 and data 17 (top peaks)
10,000 regions
format: interval, database: hg19
1.Chrom23.Start4.End5678
chr115323552515323395015324485096149.1957310.043000
chr124599475245936502460995090148.6110530.043000
chr1250572525025002507550109218.3959060.043000
chr113835125138284501383955073108.0389860.043000
chr11195288751195113001195302507097.9825340.043000
chr123055172523054055023056130074107.9559630.043000
64: CCAT on data 45 and data 17 (log)
239 lines
format: txt, database: hg19
chromosome length information read. chromNum = 94!
config file read.
fragmentSize = 150
isStrandSensitiveMode = 0
slidingWinSize = 500
movingStep = 50
75: CCAT_H3K27.bed
25,206 regions, 1 comments
format: bed, database: hg19
Info:
-----------------

read: 25206 peaks; selected: 25206
1.Chrom2.Start3.End4.Name56.Strand78910111213
track name='CCAT_H3K27' description='CCAT_H3K27'
chr115323395015324485015323552596+153233950153244850255,120,111109000
chr124593650246099502459947590+2459365024609950255,120,111163000
chr1250250025075502505725109+25025002507550255,120,11150500
chr113828450138395501383512573+1382845013839550255,120,111111000
chr111951130011953025011952887570+119511300119530250255,120,111189500
76: Probesets_FC1.5_10022011.txt
16,142 lines
format: tabular, database: mm9
Info: uploaded tabular file
12345678
geneFold.Changepvalue.adjustFC=1.5
A0610010O12Rik2.54down-regulateddown-regulated474
A0910001A06Rik0.556666667up-regulatedno-response14871
A1110002B05Rik0.51up-regulatedup-regulated796
A1110003E01Rik1.575down-regulated
A1110006G14Rik1.68down-regulated
95: Peak location distribution (png)
86.0 Kb
format: png, database: hg19
Image in png format
96: Peak location distribution (stats)
62 lines
format: tabular, database: hg19
12345
Dist_TSS% expressed genes w/ a peak in ChIP% Hexpressed genes w/ a peak in ChIP% silenced genes w/ a peak in ChIP
00.01003344481605350.003114979386165830.0275752051048314
5000.01956521739130430.007237746220797070.0373746581586144
10000.02625418060200670.01026110856619330.0417046490428441
15000.02775919732441470.01291800274851120.0444393801276208
20000.0299331103678930.01484196060467250.0462625341841386
138: expForNebula_chr1.txt
1,815 lines
format: tabular, database: hg19
Info: uploaded tabular file
1234
chrsymbolexpressionlabel
chr1AADACL317.30507619silenced
chr1AADACL422.33903333silenced
chr1ABCA448.47266359expressed
chr1ABCB1058.49113667expressed
chr1ABCD3752.1346908Hexpressed
187: Gene Stats (png)
56.1 Kb
format: png, database: hg19
Image in png format
188: Annotated Genes (ChIP)
34,054 lines
format: tabular, database: hg19
123456789101112131415161718192021222324
name chr start end strand Reg foldChange GeneBodyNormalizedScore score_Gene distTSS_Gene score_Promoter distTSS_Promoter score_ImmDown distTSS_ImmDown score_PromoterORImmDown distTSS_PromoterORImmDown score_Enhancer distTSS_Enhancer score_Intragenic distTS
S_Intragenic score_GeneDownstream distTSS_GeneDownstream score_GeneBody GeneBodyPeak_DistToTSS
SRSF10chr1_gl000191_random3891150281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3891150281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
189: .LOG for Annotated Genes
20 lines, 2 comments
format: tabular, database: hg19
1
Proportion of genes with a peak from the ChIP dataset in a given genomic region:
expressed:
Enh. Prom. Imm.Down. Intrag. GeneDown. gene TSS gene Body
0.462871287128713 0.25990099009901 0.222772277227723 0.47029702970297 0.331683168316832 0.292079207920792 0.475247524752475
Hexpressed:
Enh. Prom. Imm.Down. Intrag. GeneDown. gene TSS gene Body
194: Gene Stats (png)
46.2 Kb
format: png, database: hg19
Image in png format
195: Annotated Genes (ChIP)
34,054 lines
format: tabular, database: hg19
123456789101112131415161718192021222324
name chr start end strand Reg foldChange GeneBodyNormalizedScore score_Gene distTSS_Gene score_Promoter distTSS_Promoter score_ImmDown distTSS_ImmDown score_PromoterORImmDown distTSS_PromoterORImmDown score_Enhancer distTSS_Enhancer score_Intragenic distTS
S_Intragenic score_GeneDownstream distTSS_GeneDownstream score_GeneBody GeneBodyPeak_DistToTSS
SRSF10chr1_gl000191_random3891150281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3891150281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
196: .LOG for Annotated Genes
33 lines, 4 comments
format: tabular, database: hg19
1
Proportion of genes with a peak from the ChIP dataset in a given genomic region:
expressed:
Enh. Prom. Imm.Down. Intrag. GeneDown. gene TSS gene Body
0.462871287128713 0.25990099009901 0.222772277227723 0.47029702970297 0.331683168316832 0.292079207920792 0.475247524752475
Hexpressed:
Enh. Prom. Imm.Down. Intrag. GeneDown. gene TSS gene Body
197: Annotated Genes (Control)
34,054 lines
format: tabular, database: hg19
123456789101112131415161718192021222324
name chr start end strand Reg foldChange GeneBodyNormalizedScore score_Gene distTSS_Gene score_Promoter distTSS_Promoter score_ImmDown distTSS_ImmDown score_PromoterORImmDown distTSS_PromoterORImmDown score_Enhancer distTSS_Enhancer score_Intragenic distTS
S_Intragenic score_GeneDownstream distTSS_GeneDownstream score_GeneBody GeneBodyPeak_DistToTSS
SRSF10chr1_gl000191_random3891150281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3891150281-1Hexpressed386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
198: Gene Stats (pdf)
5.0 Kb
format: pdf, database: hg19
Image in pdf format
199: Annotated Genes (ChIP)
34,054 lines
format: tabular, database: hg19
123456789101112131415161718192021222324
name chr start end strand Reg foldChange GeneBodyNormalizedScore score_Gene distTSS_Gene score_Promoter distTSS_Promoter score_ImmDown distTSS_ImmDown score_PromoterORImmDown distTSS_PromoterORImmDown score_Enhancer distTSS_Enhancer score_Intragenic distTS
S_Intragenic score_GeneDownstream distTSS_GeneDownstream score_GeneBody GeneBodyPeak_DistToTSS
SRSF10chr1_gl000191_random3891150281-1NA10010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1NA10010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1NA10010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3891150281-1NA10010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
200: .LOG for Annotated Genes
9 lines, 3 comments
format: tabular, database: hg19
1
Proportion of genes with a peak from the ChIP dataset in a given genomic region:
Enh. Prom. Imm.Down. Intrag. GeneDown. gene TSS gene Body
0.0410159331124783 0.0259241731082715 0.0219277488562865 0.0409107640532155 0.031761055897355 0.0280275542935268 0.0420150391754746
Proportion of genes with a peak from the Control dataset in a given genomic region:
Enh. Prom. Imm.Down. Intrag. GeneDown. gene TSS gene Body
201: Annotated Genes (Control)
34,054 lines
format: tabular, database: hg19
123456789101112131415161718192021222324
name chr start end strand Reg foldChange GeneBodyNormalizedScore score_Gene distTSS_Gene score_Promoter distTSS_Promoter score_ImmDown distTSS_ImmDown score_PromoterORImmDown distTSS_PromoterORImmDown score_Enhancer distTSS_Enhancer score_Intragenic distTS
S_Intragenic score_GeneDownstream distTSS_GeneDownstream score_GeneBody GeneBodyPeak_DistToTSS
SRSF10chr1_gl000191_random3891150281-1NA10010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1NA10010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1NA10010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3891150281-1NA10010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
202: expForNebula_chr1.txt
1,815 lines
format: tabular, database: hg19
Info: uploaded tabular file
1234
chrsymbolexpressionlabel
chr1AADACL317.30507619silenced
chr1AADACL422.33903333silenced
chr1ABCA448.47266359exp_moderate
chr1ABCB1058.49113667exp_moderate
chr1ABCD3752.1346908exp_high
204: Annotated Genes (ChIP)
34,054 lines
format: tabular, database: hg19
123456789101112131415161718192021222324
name chr start end strand Reg foldChange GeneBodyNormalizedScore score_Gene distTSS_Gene score_Promoter distTSS_Promoter score_ImmDown distTSS_ImmDown score_PromoterORImmDown distTSS_PromoterORImmDown score_Enhancer distTSS_Enhancer score_Intragenic distTS
S_Intragenic score_GeneDownstream distTSS_GeneDownstream score_GeneBody GeneBodyPeak_DistToTSS
SRSF10chr1_gl000191_random3891150281-1exp_high386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1exp_high386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3627250281-1exp_high386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
SRSF10chr1_gl000191_random3891150281-1exp_high386.61232370010000000000010000000000010000000000010000000000010000000000010000000000010000000000010000000000
205: .LOG for Annotated Genes
20 lines, 2 comments
format: tabular, database: hg19
1
Proportion of genes with a peak from the ChIP dataset in a given genomic region:
exp_high:
Enh. Prom. Imm.Down. Intrag. GeneDown. gene TSS gene Body
0.189859762675297 0.101402373247033 0.0539374325782093 0.222222222222222 0.138079827400216 0.10571736785329 0.226537216828479
exp_moderate:
Enh. Prom. Imm.Down. Intrag. GeneDown. gene TSS gene Body
206: Gene Stats (pdf)
5.2 Kb
format: pdf, database: hg19
Image in pdf format
212: Peak location distribution (stats)
102 lines
format: tabular, database: hg19
12
Dist_TSS% genes w/ a peak in ChIP
00.013088699310506
1000.0146079233376183
2000.0162440107514316
3000.0178411437030112
4000.018970823107787
213: Peak location distribution (pdf)
9.9 Kb
format: pdf, database: hg19
Image in pdf format
214: Peak location distribution (stats)
102 lines
format: tabular, database: hg19
12345
Dist_TSS% expressed genes w/ a peak in ChIP% Hexpressed genes w/ a peak in ChIP% silenced genes w/ a peak in ChIP
00.1136363636363640.02773246329526920.390070921985816
1000.1325757575757580.0318107667210440.429078014184397
2000.1647727272727270.03915171288743880.453900709219858
3000.1799242424242420.05057096247960850.480496453900709
4000.1988636363636360.05628058727569330.49645390070922
215: CCAT on data 17 and data 45 (peaks)
44,101 regions
format: interval, database: hg19
1.Chrom23.Start4.End5678
chr183194258315300832400059030.5134300.001000
chr123610687523610525023610880055028.2302650.001000
chr123696875236938002370190055028.2302650.001000
chr124177417524176525024180340054027.5329430.001000
chr115117042515115585015117355054027.5329430.001000
chr141332175413279504133550053027.3192480.001000
216: CCAT on data 17 and data 45 (regions)
17,824 regions
format: interval, database: hg19
1.Chrom23.Start4.End5678
chr183194258315300832400059030.5134300.001000
chr123610687523610525023610880055028.2302650.001000
chr123696875236938002370190055028.2302650.001000
chr124177417524176525024180340054027.5329430.001000
chr115117042515115585015117355054027.5329430.001000
chr116242575162147501626085053027.3192480.001000
217: CCAT on data 17 and data 45 (top peaks)
10,000 regions
format: interval, database: hg19
1.Chrom23.Start4.End5678
chr183194258315300832400059030.5134300.001000
chr123610687523610525023610880055028.2302650.001000
chr123696875236938002370190055028.2302650.001000
chr124177417524176525024180340054027.5329430.001000
chr115117042515115585015117355054027.5329430.001000
chr141332175413279504133550053027.3192480.001000
218: CCAT on data 17 and data 45 (log)
220 lines
format: txt, database: hg19
chromosome length information read. chromNum = 94!
config file read.
fragmentSize = 150
isStrandSensitiveMode = 0
slidingWinSize = 500
movingStep = 50
219: CCAT_control.bed
17,824 regions, 1 comments
format: bed, database: hg19
Info:
-----------------

read: 17824 peaks; selected: 17824
1.Chrom2.Start3.End4.Name56.Strand78910111213
track name='CCAT_control' description='CCAT_control'
chr183153008324000831942559+83153008324000255,120,11187000
chr123610525023610880023610687555+236105250236108800255,120,11135500
chr123693800237019002369687555+2369380023701900255,120,11181000
chr124176525024180340024177417554+241765250241803400255,120,111381500
chr115115585015117355015117042554+151155850151173550255,120,111177000
220: Peak location distribution (pdf)
7.1 Kb
format: pdf, database: hg19
Image in pdf format
221: Peak location distribution (stats)
102 lines
format: tabular, database: hg19
123
Dist_TSS% genes w/ a peak in ChIP% genes w/ a peak in control
00.0130886993105060.0462389466713412
3000.01784114370301120.0564060613143236
6000.02130809084180590.0606131432355576
9000.02415176658486230.0633010011296794
12000.02582680846090920.0652876787035955
222: Peak location distribution (pdf)
12.5 Kb
format: pdf, database: hg19
Image in pdf format
223: Peak location distribution (stats)
502 lines
format: tabular, database: hg19
12
Dist_TSS% genes w/ a peak in ChIP
00.013088699310506
1000.0146079233376183
2000.0162440107514316
3000.0178411437030112
4000.018970823107787