Hello everyone, I have a simple question about generic paired-end Illumina data. If one read of a pair is unmapped, does this automatically mean that the pair is improper and is (un)flagged in a SAM file?
Thanks!
Thanks!
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Flag Chr Description 0x0001 p the read is paired in sequencing 0x0002 P the read is mapped in a proper pair 0x0004 u the query sequence itself is unmapped 0x0008 U the mate is unmapped 0x0010 r strand of the query (1 for reverse) 0x0020 R strand of the mate 0x0040 1 the read is the first read in a pair 0x0080 2 the read is the second read in a pair 0x0100 s the alignment is not primary 0x0200 f the read fails platform/vendor quality checks 0x0400 d the read is either a PCR or an optical duplicate
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