Hi . I am using 'TABLET SEQUENCE VIEWER' now. but I don't really understand about difference between 'clipping' and 'unmapped' and 'skipped' with CIGAR. And if any CIGAR value is '36S76M" , then what's going on 37~75 base?? Thank you.
Unmapped information always shows in FLAG with 0x4, with no information in CIGAR.
clipping(S/H) and skipped(N) information shows in CIGAR.
Taking an example,
if read A is unmapped, it's FLAG includes 4(Bit) and it's CIGAR is '*'.
if read A is mapped, but only part of it is mapped, it's FLAG does not include 4(Bit) and it's CIGAR is like '36S76M'(means 36nts is unmapped to reference but these soft-chipped sequences are stored in SEQ).
- A simaliar concept is hard clipping(H) (clipped sequences NOT present in SEQ).So H can only be present as the first and/or last operation.S may only have H operations between them, or be present as the end of the CIGAR string(such as 3S89M,67M43S,31S56M21S).
- if read A is mapped, but parts of it are mapped to different position, which include a long gap between each of part,it's CIGAR is like 56M1200N63M.
- For mRNA, an N operation always represents an intron.