Collin Rna-seq for two groups

Annotation:

StepAnnotation
Step 1: Input dataset collection
select at runtime
Step 2: Input dataset collection
select at runtime
Step 3: Input dataset
select at runtime
Step 4: FASTQ Groomer
Output dataset 'output' from step 1
Sanger & Illumina 1.8+
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Step 5: FASTQ Groomer
Output dataset 'output' from step 2
Sanger & Illumina 1.8+
Hide Advanced Options
Step 6: Trimmomatic
Paired-end (as collection)
Output dataset 'output_file' from step 4
True
TruSeq3 (paired-ended, for MiSeq and HiSeq)
2
30
10
Trimmomatic Operations
Trimmomatic Operation 1
Cut bases off the start of a read, if below a threshold quality (LEADING)
3
Trimmomatic Operation 2
Cut bases off the end of a read, if below a threshold quality (TRAILING)
3
Trimmomatic Operation 3
Sliding window trimming (SLIDINGWINDOW)
4
20
Trimmomatic Operation 4
Drop reads below a specified length (MINLEN)
36
Use default job resource parameters
Step 7: Trimmomatic
Paired-end (as collection)
Output dataset 'output_file' from step 5
True
TruSeq3 (paired-ended, for MiSeq and HiSeq)
2
30
10
Trimmomatic Operations
Trimmomatic Operation 1
Cut bases off the start of a read, if below a threshold quality (LEADING)
3
Trimmomatic Operation 2
Cut bases off the end of a read, if below a threshold quality (TRAILING)
3
Trimmomatic Operation 3
Sliding window trimming (SLIDINGWINDOW)
4
20
Trimmomatic Operation 4
Drop reads below a specified length (MINLEN)
36
Use default job resource parameters
Step 8: FastQC
Output dataset 'fastq_out_paired' from step 6
select at runtime
select at runtime
Module to evaluate the fastq after pre processing, comparison to former module possible.
Step 9: RNA STAR
Paired-end (as collection)
Output dataset 'fastq_out_paired' from step 6
Use a built-in index
use genome reference without builtin gene-model
hg38
Output dataset 'output' from step 3
100
True
No
Use Defaults
Step 10: FastQC
Output dataset 'fastq_out_paired' from step 7
select at runtime
select at runtime
Step 11: RNA STAR
Paired-end (as collection)
Output dataset 'fastq_out_paired' from step 7
Use a built-in index
use genome reference without builtin gene-model
hg38
Output dataset 'output' from step 3
100
True
No
Use Defaults
Step 12: DESeq2
Factors
Factor 1
Empty.
Factor levels
Factor level 1
Control
Output dataset 'reads_per_gene' from step 9
Factor level 2
Myasthenic
Output dataset 'reads_per_gene' from step 11
Count data (e.g. from htseq-count or feature-count)
True
True
False
parametric
False
False
False
Use default job resource parameters