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Published Workflows | puva | W1 - Pre-processing | Paired-end

Galaxy Workflow ' W1 - Pre-processing | Paired-end'

Annotation: Pre-processing of paired-end reads

StepAnnotation
Step 1: Input dataset
select at runtime
Forward reads in Fastq format
Step 2: Input dataset
select at runtime
Reverse reads in Fastq format
Step 3: FASTQ Groomer
Output dataset 'output' from step 1
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Convert forward reads to fastqsanger encoding
Step 4: FASTQ Groomer
Output dataset 'output' from step 2
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Convert reverse reads to fastqsanger encoding
Step 5: FastQC:Read QC
Output dataset 'output_file' from step 3
QC forward reads - raw
select at runtime
Quality control of forward reads
Step 6: FastQC:Read QC
Output dataset 'output_file' from step 4
QC reverse reads - raw
select at runtime
Quality control of reverse reads
Step 7: FASTQ positional and quality trimming
Paired-end
Output dataset 'output_file' from step 3
Output dataset 'output_file' from step 4
20
20.0
Trimming/filtering based on sequence quality and length
Step 8: Paired-end compositional filtering
Output dataset 'trimmed1' from step 7
Output dataset 'trimmed2' from step 7
80.0
30.0
20.0
Filter reads based on frequency of monomers, dimers and trimers
Step 9: FastQC:Read QC
Output dataset 'lefttrimmed' from step 8
QC forward reads - processed
select at runtime
Quality control of filtered reads
Step 10: FastQC:Read QC
Output dataset 'righttrimmed' from step 8
QC reverse reads - processed
select at runtime
Quality control of filtered reads
Step 11: Concatenate datasets
Output dataset 'unmating' from step 8
Datasets
Dataset 1
Output dataset 'trimmedunpaired' from step 7
Dataset 2
Output dataset 'discarded' from step 8
Concatenate filtered reads from previous steps