NonSpliced RNAseq workflow
Version 1

Work-in-progress

Workflow for NonSpliced RNAseq data with multiple aligners.

Steps:

- workflow_quality.cwl:

    - FastQC (control)

    - fastp (trimming)

- bowtie2 (read mapping)

- sam_to_sorted-bam

- featurecounts (transcript read counts)

- kallisto (transcript [pseudo]counts)

Inputs

ID Name Description Type
threads number of threads number of threads to use for computational processes int?
memory Max memory maximum memory usage in megabytes int?
filter_rrna Filer rRNA Filter rRNA from reads if true boolean
prefix_id Filename prefix Prefix of the output filenames. string
forward_reads forward reads forward sequence file locally File
reverse_reads reverse reads reverse sequence file locally File
bowtie2-indexfolder bowtie2 index Folder location of the bowtie2 index files. Directory
kallisto-indexfolder kallisto index Folder location of the kallisto index file. Directory?
gtf GTF file GTF file location File?

Steps

ID Name Description
quality Quality and filtering workflow Quality assessment of illumina reads with rRNA filtering option
bowtie2 bowtie2 runs bowtie2 alignment on the genome with the quality filtered reads.
sam_to_sorted-bam sam to sorted bam Converts a SAM file to a sorted BAM file
featurecounts FeatureCounts Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts.
kallisto kallisto Calculates transcript abundances
bowtie2_files_to_folder bowtie2 output Preparation of bowtie2 output files to a specific output folder
featurecounts_files_to_folder FeatureCounts output Preparation of FeatureCounts output files to a specific output folder
kallisto_files_to_folder FeatureCounts output Preparation of kallisto output files to a specific output folder

Outputs

ID Name Description Type
files_to_folder_fastqc FASTQC Quality reporting by FASTQC Directory
files_to_folder_filtered Filtered reads folder Output folder with filtered reads. Directory
files_to_folder_bowtie2 bowtie2 output bowtie2 mapping results folder. Contains sorted bam file, metrics file and mapping statistics (stdout). Directory
files_to_folder_featurecounts FeatureCounts output FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout). Directory
files_to_folder_kallisto kallisto output kallisto results folder. Contains transcript abundances, run info and summary. Directory
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Views: 270   Downloads: 17

Created: 24th Nov 2020 at 11:05

Last updated: 22nd Dec 2020 at 15:55

Last used: 20th Apr 2021 at 02:44

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Version History

Version 1 Created 24th Nov 2020 at 11:05 by Bart Nijsse

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