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Published Workflows | vboeva | Nebula test 2014 Histones
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Galaxy Workflow ' Nebula test 2014 Histones'


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_H3K27me3
select at runtime
Step 5: flagstat
Output dataset 'output' from step 1
Step 6: Convert from BAM to BED
Output dataset 'output' from step 1
Create a 6-column BED file.
False
False
Step 7: flagstat
Output dataset 'output' from step 2
Step 8: Fastqc: Fastqc QC
Output dataset 'output' from step 2
FastQC_input
select at runtime
Step 9: MACS
MAC_H3K27me3
Single End
Output dataset 'output' from step 1
Output dataset 'output' from step 2
240000000.0
75
300
0.001
10,30
False
Save
20
False
Do not build the shifting model
75
Do not produce report (faster)
Step 10: Convert from BAM to BED
Output dataset 'output' from step 2
Create a 6-column BED file.
False
False
Step 11: Wig-to-bigWig
Output dataset 'output_treatment_wig_file' from step 9
Default
Step 12: Wig-to-bigWig
Output dataset 'output_control_wig_file' from step 9
Default
Step 13: CCAT
Output dataset 'output' from step 6
Output dataset 'output' from step 10
Show Advanced Options
150
500
50
Local maximum of read-enrichment profile
4
10000
123456
2.0
50
Step 14: Convert CCAT output (intervals) into Bed
CCAT_H3K27me3
Output dataset 'output_region_file' from step 13
0
Step 15: Annotation of genes with ChIP-seq peaks (histones)
Output dataset 'output' from step 14
No
-1000
1000
-30000
5000
Homo sapiens
hg19
Yes
Output dataset 'output' from step 3
False
Step 16: Get peak distribution around TSS (Histones)
Output dataset 'output' from step 14
No
500
50000
Homo sapiens
hg19
Yes
Output dataset 'output' from step 3
False