Samtools difference between Mapped and Unmapped read
Hello,
I am wondering what the difference is between a mapped and unmapped read in samtools.
I am extremely new to this whole process, just trying to learn my way through so if you could "dumb" it down or try and explain it in a simpler way that would be helpful. Thank you
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WouterDeCoster
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Sean •
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While it is not light reading it may help to take a look at the SAM file format specification. Mandatory fields in alignments are in section 1.4. Field number three refers to "Reference Name".
Otherwise there will be the name of reference segment the read aligns to e.g.
chr1.A mapped read is a read for which the aligner could find a fitting spot in the genome (an alignment). For an unmapped read, no suitable alignment was found.