3.1 years ago by
For RNA-seq data, the minimum QA needed in order to map the data successfully is the goal (to avoid introducing bias into the experiment).
Run the tool FastQC first to determine if there are regions of the sequence that would benefit from trimming (low quality ends that would interfere with mapping success). Then use this tool or one of the others that directly clip/trim regions of sequence in the same tool group (NGS: QC and manipulation).
Then map the data. You could take a sample, run the QA a few different ways, map and then compare mapping rates to determine the best QA for your particular datasets.
Also see: GalaxyNGS101#Fastq_manipulation_and_quality_control
Thanks, Jen, Galaxy team