In paired end mode chimeric pairs are labeled as discordant and thrown out. How does Bowtie2 handle chimeric singletons? Lets say you map only R1 reads and some of the reads map to different chromosomes, depending on the side of the singleton. Does this R1 singleton get a low mapping score or does bowtie2 label it as a chimera somehow?
It appears BWA-mem labels these as "SA:" in a sam file. Anything similar happening in Bowtie2?
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jnowacki
1 answer
bowtie2 doesn't throw out reads from a pair that align to different chromosomes if you specify --no-mixed.
Bowtie2 doesn't handle chimeric single-end reads. If you use the default end-to-end mode then these won't align. If you use local alignment, then these will sometimes align to at least one of the possible locations, but the flag for a chimeric (supplementary) alignment will never be set.
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