uab-cgds-worthey/quac

Need to refactor fastq_screen testing in QuaC Watch?

ManavalanG opened this issue · 1 comments

ManavalanG commented

Pa**** samples of muscular dystrophy project were affected by mouse contamination (albeit seemingly only at exons of about 100-300 genes), but QuaC watch's fastq-screen testing didn't pick it up. It appears this may have been due to a relatively smaller amount of contamination as well as the contamination regions being non-random.

However, columns #One_hit_one_genome and #Multiple_hits_one_genome from fastq_screen results may be able to identify this contamination. Here is the comparison that shows this pattern.