What's the difference between half mapped reads and single paired reads?

Question

[omariqbal2017]

I'm new in the SAM file format and I need to know what are the main difference between a half mapped read and a single paired read, and if possible also need to know how to detect this differences in the flag of the read.

[GenoMax]

Do you mean a read that is partially mapped (soft clipped)? Each of the reads in a paired-end pair could qualify for this condition.

Answer 1

[d-cameron]

Your terminology is not standard so I'm not sure what you are referring to. You are possibly asking the different between soft clipped reads and read pairs in which a single read is mapped.

Clipped read: An individual read only partially aligns. The bases which do not align are known as 'clipped' bases which can either be soft clipped (included in the read sequence), or hard clipped (removed from the read - used by bwa mem chimeric split read supplementary alignments to save space since the full sequence is available in the primary alignment record). For example a read alignment CIGAR of 100M indicates the entire read maps, 50M50S indicates that only the first half of the read maps. There no special flags for these and you need to look at the CIGAR field.

Read pair in which only one of the reads is mapped: there is no commonly accepted terminology for these, although dangling reads, and one-end-anchored (OEA) read pairs are used in multiple papers. These reads can be identified by the flag combination of 0x1 set, 0x4 not set, and 0x8 set.

See section 1.4.2 for flag details https://samtools.github.io/hts-specs/SAMv1.pdf