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Published Workflows | vboeva | Workflow from 'Nebula Test TF 2015'
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Galaxy Workflow ' Workflow from 'Nebula Test TF 2015''


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: Fastqc: Fastqc QC
Output dataset 'output' from step 1
FastQC
select at runtime
Step 5: Filter BAM
Output dataset 'output' from step 1
20
Step 6: Fastqc: Fastqc QC
Output dataset 'output' from step 2
FastQC
select at runtime
Step 7: Filter BAM
Output dataset 'output' from step 2
20
Step 8: flagstat
Output dataset 'filteredBam' from step 5
Step 9: MACS
MACS chr1
Single End
Output dataset 'filteredBam' from step 5
Output dataset 'filteredBam' from step 7
1880000000.0
50
200
1e-05
7,40
True
Save
10
False
Do not build the shifting model
100
Do not produce report (faster)
Step 10: Get Subset for ChIP Control
BAM
Output dataset 'filteredBam' from step 5
Output dataset 'filteredBam' from step 7
True
Step 11: flagstat
Output dataset 'filteredBam' from step 7
Step 12: Extract regions around peak maxima for a .bed file with peak coordinates
Output dataset 'output_xls_to_interval_peaks_file' from step 9
No
200
Step 13: FindPeaks
SAM/BAM
105
90
120
3
0.2
False
Output dataset 'BAMcontrolOutBAM' from step 10
Input
Step 14: FindPeaks
SAM/BAM
105
90
120
3
0.2
False
Output dataset 'BAMsampleOutBAM' from step 10
TF
Step 15: fastaFromBed
Mus musculus
mm9
Output dataset 'output' from step 12
Step 16: Get peak height distribution
Output dataset 'peaks' from step 14
Output dataset 'peaks' from step 13
3
50
No
Step 17: Filter FindPeaks output (.peaks) using Control Peaks
Output dataset 'peaks' from step 14
Output dataset 'peaks' from step 13
10
4
1.6
Yes
TF_FindPeaks
Input_Findpeaks
Step 18: (di)ChIPmunk
FP_200bp
Output dataset 'fastaOut' from step 15
MonoChIPMunk
Mono
Simple
3
10
15
mask
Step 19: Extract regions around peak maxima for a .bed file with peak coordinates
Output dataset 'outputB' from step 17
No
200
Step 20: Genomic annotation of Chip-Seq peaks
Output dataset 'outputB' from step 17
0.0
Yes
Output dataset 'outputBC' from step 17
-2000
2000
-30000
5000
Mus musculus
mm9
Yes
Output dataset 'output' from step 3
False
Step 21: Annotation of genes with ChIP-seq peaks (transcription factors)
Output dataset 'outputB' from step 17
Yes
Output dataset 'outputBC' from step 17
do not use bootstrap resampling
-2000
2000
-30000
5000
Mus musculus
mm9
Yes
Output dataset 'output' from step 3
False
Step 22: Get peak distribution around TSS (Transcription factors)
Output dataset 'outputB' from step 17
Yes
Output dataset 'outputBC' from step 17
1000
50000
Mus musculus
mm9
Yes
Output dataset 'output' from step 3
False
Step 23: fastaFromBed
Mus musculus
mm9
Output dataset 'output' from step 19
Step 24: Filter
Output dataset 'stats' from step 20
(c7=='promoter' or c7=='immediateDownstream') and c9=='up-regulated'
Step 25: (di)ChIPmunk
FP_promoterUP
Output dataset 'fastaOut' from step 23
MonoChIPMunk
Mono
Simple
3
10
15
mask
Step 26: Extract regions around peak maxima for a .bed file with peak coordinates
Output dataset 'out_file1' from step 24
No
300
Step 27: fastaFromBed
Mus musculus
mm9
Output dataset 'output' from step 26
Step 28: (di)ChIPmunk
MACS_200bp
Output dataset 'fastaOut' from step 27
MonoChIPMunk
Mono
Simple
3
10
15
mask