Does Every Read In Paired-End Sam File Have The 0X0001 Flag?

Question

[mrals89]

Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag?

Thanks!

Answer 1

[Istvan Albert]

The paired flag indicates that in this file the read is paired and both pairs are present.

An aligner may choose to not include both pairs, even though the original data were paired. Also the concept of pairing makes sense in terms of fragment sizes and semi global alignments. If you have a spliced alignment it is not clear what the template size is/should be.

An interesting shortcut to remember: paired data turns flags into odd numbers.