what does CIGAR '22M2007N79M-61p82M19S' means?

Question

[juncheng]

Hi,

This cigar is from paired end 101bp RNA-seq data.

I kind of know the others, but especially what does -61p means? The '-' here means minus?

Best

[Devon Ryan]

That shouldn't exist, can you post the whole alignment (just that one line)?

[Devon Ryan]

BTW, this actually just looks like a corrupt line.

[juncheng]

Yes, you are right. I found it only appears in the Chimeric.out.junction file of STAR. The STAR develop group might can explain.

Answer 1

[juncheng]

Note, that unlike standard SAM, both mates are recorded in one line here. The gap of length L between the mates is marked by the "Lp" in the CIGAR string.

If the mates overlap, L<0.

That's the explanation. Thanks @Devon Ryan

[Devon Ryan]

Guess we replied at the same time. Yes, STAR doesn't use the same CIGAR format in that file that's used in SAM/BAM files.

Answer 2

[Devon Ryan]

In the future, you might want to mention at the beginning that this CIGAR string is coming from STAR's chimeric.out.junction file. The format of that file is described here and that string only makes sense it that context (i.e., it's not a regular CIGAR string). So the string describes both mates and the -61p is the distance between the mates, where a negative value means the mates overlap.