sequence and germline start

[ape...@gmail.com]

Hey,

I'm getting different numbers for the V,D, and J sequence start and V germline start then I would expect.It seems that it takes into account the Ns, though i'm not sure.

Should I always subtract the number of Ns from the 'sequence', and 'sequence alignment' to get the correct numbering?

Thanks,

Ayelet

[Duncan Ralph]

I'm not sure that I'm interpreting this correctly -- it might be safer to give an example. But in general if there's a coordinate specifying the start or end of something in a sequence, yes, it includes all bases/positions in the sequence, not just ACGT. So, for instance, in python slice notation you'd go seq[start : end], rather than trying to remove particular bases before applying the start/end indices.

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