I'm trying to understand Minimap2 output. The mapped reads include paired reads (interlaced), with singletons mixed within these results. I'm trying to understand this, and how to use the output. Can I use these reads directly into Metaspades, paired with singletons??
I'm guessing that what I'm seeing are what it classifies as a chimeric sequence, where only one strand matches, so the mapped reads will include single end where only one read matches the reference, and other other goes as a single read as unmapped??
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written
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Jon •
1 answer
Minimap 2 has two outputs the PAF format and the SAM format.
Each has a documentation that describes how the information is encoded. In general paried-end input will generate paired-end output. Supplementary alignments (chimeric) alignments typically refer to situations where complementary regions of the SAME read align to different,potentially distant regions in the genome.
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