Cigar String - Are Soft Clipped Reads Only Ever At The Start Or End?

Question

[Clare]

Forgive this basic question, but with a cigar string, are soft clipped reads only ever seen at the start or end of the read and cigar string? i.e. 2S80M or 80M1D5S NOT 20M5S30M

[Istvan Albert]

otherwise wouldn't be clip but an insertion relative to the reference. one cannot ascertain an insertion if it is at the end of the read hence the new terminology of clipping

Answer 1

[cts]

Yep that's correct the sam specification says that 'S' can only be found ate the ends of reads

Answer 2

[Ashutosh Pandey]

To the best of my knowledge you are right. You will never see them in the middle of the read. They should be present either at the start or the end or both. RNAseq (splice aware) aligners use "N" as a cigar character to show the distance between the split parts of the same read.