Does anyone know if BWA gives ambiguous reads a mapping quality score of 0? I believe I have read somewhere that it does, but I can't find this anywhere in the BWA documentation. (Actually, the only documentation I've found for BWA are the man page and the FAQ page. Is there more somewhere?) The FAQ page does mention that for paired-end reads, one read may have a mapping quality of 0 if it is ambiguous, and the other end can be non-zero. But are all ambiguous reads assigned a mapping quality of 0? Thanks!
-
-
That is correct. If a read maps to two or more places with equal score it is given a mapping quality of zero. Depending on the input options, it will output a random mapping or all mappings.Originally posted by kweber2 View Post -
Thank you very much! -KrisComment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment