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Galaxy Workflow ' ChIP-seq analysis'


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Fastqc: Fastqc QC
Output dataset 'output' from step 1
FastQC
select at runtime
Quality check
Step 3: Map with Bowtie for Illumina
Use a built-in index
hg19
Single-end
Output dataset 'output' from step 1
Full parameter list
0
-1
0
0
2
70
28
Round to nearest 10
-1
Do not try hard
1
Do not report all valid alignments
-1
False
False
Do not use best
125
-1
-1
False
Map reads to genome
Step 4: SAM-to-BAM
BAM_file
Locally cached
Output dataset 'output' from step 3
Convert SAM to BAM
Step 5: MACS
MACS in Galaxy without wiggle without report
Single End
Output dataset 'output1' from step 4
select at runtime
2700000000.0
25
300
1e-05
10,30
False
Do not create wig file (faster)
False
Do not build the shifting model
100
Do not produce report (faster)
Peak calling
Step 6: Get peak distribution around TSS (Transcription factors)
Output dataset 'output_bed_file' from step 5
No
1000
50000
Homo sapiens
hg19
No
True
Step 7: Annotation of genes with ChIP-seq peaks (transcription factors)
Output dataset 'output_bed_file' from step 5
No
-2000
2000
-30000
5000
Homo sapiens
hg19
No
True
Step 8: Genomic annotation of Chip-Seq peaks
Output dataset 'output_bed_file' from step 5
0.0
No
-2000
2000
-30000
5000
Homo sapiens
hg19
No
False