Accessible Workflow | imported: RNASeq_Step1_SecondaryAnalysis

Galaxy Workflow ' imported: RNASeq_Step1_SecondaryAnalysis'


StepAnnotation
Step 1: Input dataset
select at runtime
Raw fastq files. Phred score Sanger scaled. Illumina 1.8 and later.
Step 2: Input dataset
select at runtime
GTF file compatible with genome reference sequences
Step 3: Trimmomatic
True
Pair of datasets
Output dataset 'output' from step 1
Output dataset 'output' from step 1
True
TruSeq3 (paired-ended, for MiSeq and HiSeq)
2
30
10
Trimmomatic Operations
Trimmomatic Operation 1
Cut bases off the end of a read, if below a threshold quality (TRAILING)
10
Trimmomatic Operation 2
Drop reads below a specified length (MINLEN)
20
Step 4: TopHat
Paired-end (as individual datasets)
Output dataset 'fastq_out_r1_paired' from step 3
Output dataset 'fastq_out_r2_paired' from step 3
30
150
No
Use a built-in genome
<galaxy.tools.parameters.basic.RuntimeValue object at 0x7ff768516410>
Full parameter list
1000
2
FR First Strand
2
No
8
Not available.
70
500000
Yes
3
3
20
50
500000
2
25
Not available.
No
Auto
No
No
No
No
Step 5: Sort
Output dataset 'accepted_hits' from step 4
Read names (-n)
BAM files need to be sorted to run HTSeq
Step 6: htseq-count
Output dataset 'output1' from step 5
Output dataset 'output' from step 2
Union
Yes
10
exon
gene_id
Not available.
Not available.