Galaxy Workflow ' RNASeq Analysis'

Annotation:

StepAnnotation
Step 1: Input dataset
select at runtime
asp5_leaf_read1.P001.fq
Step 2: Input dataset
select at runtime
asp5_leaf_read2.P001.fq
Step 3: Input dataset
select at runtime
asp5_xylem_read1.P001.fq
Step 4: Input dataset
select at runtime
asp5_xylem_read2.P001.fq
Step 5: PopGenIE random fastq extract tool
Output dataset 'output' from step 1
Output dataset 'output' from step 2
Step 6: PopGenIE random fastq extract tool
Output dataset 'output' from step 3
Output dataset 'output' from step 4
Step 7: FASTQ Groomer
Output dataset 'output1' from step 5
Sanger
Hide Advanced Options
Step 8: FASTQ Groomer
Output dataset 'output2' from step 5
Sanger
Hide Advanced Options
Step 9: FASTQ Groomer
Output dataset 'output1' from step 6
Sanger
Hide Advanced Options
Step 10: FASTQ Groomer
Output dataset 'output2' from step 6
Sanger
Hide Advanced Options
Step 11: Trim sequences
Output dataset 'output_file' from step 7
10
90
Step 12: Fastqc: Fastqc QC
Output dataset 'output_file' from step 7
FastQC
select at runtime
Step 13: Trim sequences
Output dataset 'output_file' from step 8
10
90
Step 14: Fastqc: Fastqc QC
Output dataset 'output_file' from step 8
FastQC
select at runtime
Step 15: Fastqc: Fastqc QC
Output dataset 'output_file' from step 9
FastQC
select at runtime
Step 16: Trim sequences
Output dataset 'output_file' from step 9
10
90
Step 17: Fastqc: Fastqc QC
Output dataset 'output_file' from step 10
FastQC
select at runtime
Step 18: Trim sequences
Output dataset 'output_file' from step 10
10
90
Step 19: Tophat
Use a built-in index
Populus_unmasked
Paired-end
Output dataset 'output' from step 11
Output dataset 'output' from step 13
20
Commonly used
Step 20: Tophat
Use a built-in index
Populus_unmasked
Paired-end
Output dataset 'output' from step 16
Output dataset 'output' from step 18
20
Commonly used
Step 21: Cufflinks
Output dataset 'accepted_hits' from step 19
300000
0.05
0.05
No
No
No
No
Step 22: Cufflinks
Output dataset 'accepted_hits' from step 20
300000
0.05
0.05
No
No
No
No
Step 23: Cuffcompare
Output dataset 'assembled_isoforms' from step 21
Additional GTF Input Files
Additional GTF Input Files 1
Output dataset 'assembled_isoforms' from step 22
Yes
select at runtime
False
No
Step 24: Cuffdiff
Output dataset 'transcripts_combined' from step 23
No
Output dataset 'accepted_hits' from step 19
Output dataset 'accepted_hits' from step 20
0.05
1000
No
No
No