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Published Histories | vboeva | Nebula test 2014 Histones
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Galaxy History ' Nebula test 2014 Histones'


DatasetAnnotation
1: expForNebula_chr1.txt
1,815 lines
format: tabular, database: hg19
1234
chrsymbolexpressionlabel
chr1AADACL317.30507619silenced
chr1AADACL422.33903333silenced
chr1ABCA448.47266359exp_moderate
chr1ABCB1058.49113667exp_moderate
chr1ABCD3752.1346908exp_high
2: H3K27me3_chr1.sorted.noDup.bam
256.9 Mb
format: bam, database: hg19
Binary bam alignments file
3: Input_for_H3K27me3_chr1.sorted.noDup.bam
283.9 Mb
format: bam, database: hg19
Binary bam alignments file
4: flagstat on data 3
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: flagstat on data 2
11 lines
format: txt, database: hg19
7891807 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
7891807 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
6: FastQC_H3K27me3.html
12.3 Kb
format: html, database: hg19
HTML file
7: FastQC_input.html
12.2 Kb
format: html, database: hg19
HTML file
8: MACS on data 3 and data 2 (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
9: MACS on data 3 and data 2 (treatment: wig)
~11,000,000 lines
format: wig, database: hg19
12
track type=wiggle_0 name="MAC_H3K27me3_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
10: MACS on data 3 and data 2 (control: wig)
~12,000,000 lines
format: wig, database: hg19
12
track type=wiggle_0 name="MAC_H3K27me3_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
11: MACS on data 3 and data 2 (html report)
4.8 Kb
format: html, database: hg19
HTML file
12: Wig-to-bigWig on data 9
32.3 Mb
format: bigwig, database: hg19
display at UCSC main
Binary UCSC BigWig file
13: Wig-to-bigWig on data 10
34.7 Mb
format: bigwig, database: hg19
display at UCSC main
Binary UCSC BigWig file
14: 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-
15: 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-
16: CCAT on data 14 and data 15 (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
17: CCAT on data 14 and data 15 (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
18: CCAT on data 14 and data 15 (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
19: CCAT on data 14 and data 15 (log)
239 lines
format: txt, database: hg19
chromosome length information read. chromNum = 94!
config file read.
fragmentSize = 150
isStrandSensitiveMode = 0
slidingWinSize = 500
movingStep = 50
20: CCAT_H3K27me3.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_H3K27me3' description='CCAT_H3K27me3'
chr115323395015324485015323552596+153233950153244850255,120,111109000
chr124593650246099502459947590+2459365024609950255,120,111163000
chr1250250025075502505725109+25025002507550255,120,11150500
chr113828450138395501383512573+1382845013839550255,120,111111000
chr111951130011953025011952887570+119511300119530250255,120,111189500
21: Peak location distribution (png)
87.8 Kb
format: png, database: hg19
Image in png format
22: Peak location distribution (stats)
102 lines
format: tabular, database: hg19
12345
Dist_TSS% exp_high genes w/ a peak in ChIP% exp_moderate genes w/ a peak in ChIP% silenced genes w/ a peak in ChIP
00.02773246329526920.1136363636363640.390070921985816
5000.06443719412724310.2215909090909090.517730496453901
10000.09135399673735730.2973484848484850.574468085106383
15000.1150081566068520.3143939393939390.609929078014184
20000.1321370309951060.3390151515151510.634751773049645
23: Gene Stats (png)
56.3 Kb
format: png, database: hg19
Image in png format
24: 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
25: .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