tools_strandedness_check.cwl

Documentation for strandedness_check.cwl

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Overview

runs how_are_we_stranded_here to determine RNAseq data strandedness

Introduction

Uses how_are_we_stranded_here, a python package for testing strandedness. Runs Kallisto and Rseqc (infer-experiment-py) to to check which direction reads align once mapped in transcripts. It first creates a Kallisto index (or uses a pre-made index) of your organism's transcriptome. It then maps a small subset of reads (default 200000) to the transcriptome and uses Kallisto's --genomebam argument to project pseudoalignments to the genome sorted BAM file. (Currently only Kallisto version 0.44.0 works well with how_are_we_stranded_here.) It finally runs RSeQC's infer_experiment.py to check which direction reads from the first and second pairs are aligned in relation to the transcript strand, and provides output with the likely strandedness of your data.

Docker Requirement

mgibio/checkstrandedness:v1

Inputs

Name	Label	Description	Type	Secondary Files
reference_annotation			File
kallisto_index			File
cdna_fasta			File
reads1			File
reads2			File

Outputs

Name	Label	Description	Type	Secondary Files
strandedness_check			stdout