WebJun 7, 2024 · My understanding of BWA's output is that if a read maps perfectly to multiple genomic locations, it will be given a high mapping quality (MAPQ) score for both locations. Many people expect that a read that maps to at least two locations can have (at best) a 50% probability of mapping to one of those locations (i.e. MAPQ = 3). http://www.acgt.me/blog/2014/12/16/understanding-mapq-scores-in-sam-files-does-37-42
Understanding MAPQ scores in SAM files: does 37 = 42?
WebAug 31, 2024 · A MAPQ score of 2 is an incorrect mapping probability of 63% (i.e. close to 3 different locations), and a MAPQ of 1 is an incorrect mapping probability of 79% (close to … WebMay 29, 2014 · This behavior is the expected behavior in deterministic mode, where bowtie2 uses the read name, sequence, and quality string to seed the pseudo-random number generator. The solution would be to use the --non-deterministic flag. The real experiment would have been to change the read's name each time. chiwawa vector
Tuning bowtie2 for better performance - Arm Community
WebJan 17, 2024 · Clarified support for overriding presets with more specific options e.g bowtie2 -x index --local --very-fast-local --L22 -q reads.fq will set the seed length to 22, … WebMay 15, 2013 · I was wondering how (precisely) is calculated the MAPQ (mapping quality) value by bowtie2. The manual says : a mapping quality: a non-negative integer Q = -10 … WebApr 25, 2024 · When mapping with bowtie2 against this database, most of the reads that are mapped to one of these genomes have a MAPQ score of 0. Only at the positions that are … chiwawa tricolore