Workflow for NonSpliced RNAseq data with multiple aligners.
- workflow_quality.cwl: - FastQC (control) - fastp (trimming) - bowtie2 (read mapping) - sam_to_sorted-bam - featurecounts (transcript read counts) - kallisto (transcript [pseudo]counts)
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|number of threads
|number of threads to use for computational processes
|maximum memory usage in megabytes
|Filter rRNA from reads if true
|Prefix of the output filenames.
|forward sequence file locally
|reverse sequence file locally
|Folder location of the bowtie2 index files.
|Folder location of the kallisto index file.
|GTF file location
|Quality and filtering workflow
|Quality assessment of illumina reads with rRNA filtering option
|runs bowtie2 alignment on the genome with the quality filtered reads.
|sam to sorted bam
|Converts a SAM file to a sorted BAM file
|Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts.
|Calculates transcript abundances
|Preparation of bowtie2 output files to a specific output folder
|Preparation of FeatureCounts output files to a specific output folder
|Preparation of kallisto output files to a specific output folder
|Quality reporting by FASTQC
|Filtered reads folder
|Output folder with filtered reads.
|bowtie2 mapping results folder. Contains sorted bam file, metrics file and mapping statistics (stdout).
|FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout).
|kallisto results folder. Contains transcript abundances, run info and summary.
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Created: 24th Nov 2020 at 11:05
Last updated: 8th Jun 2021 at 08:32