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

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

chip-seq
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updated by Ram Ram • written by juncheng juncheng

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

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updated by Ram Ram • written by Devon Ryan Devon Ryan

BTW, this actually just looks like a corrupt line.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

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

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updated by Ram Ram • written by juncheng juncheng

2 answers

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

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updated by Ram Ram • written by juncheng juncheng

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.

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updated by Ram Ram • written by Devon Ryan 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.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

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