Why don't the aligned read files have quality scores?

Quality scores take up the majority of space in our compressed sequence files, so removing them makes the files much smaller (~80% or more). In addition, many uses don’t require per-base quality scores to successfully complete their work (some pipelines even require fastq format but don’t actually use the quality scores), so these files represent a faster route to completing many analyses. The full quality scores are still available in the original SRA Runs for anyone that requires them, using the SRA Tools available in Galaxy.

Still have questions?

Want to embed this snippet (FAQ) in your GTN Tutorial?

{% snippet  topics/galaxy-interface/tutorials/ncbi-sarf/faqs/quality-scores.md %}