Hi, CREST reports at individual base pair resolution the left and right breakpoint but in the case of translocations I don't understand how to determine how large the SV is as these positions only inform one of where the the SV is and where it moved to if I understand this correctly. Can anyone who understands this better than I do offer me their insights into solving this problem?
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Also wondering
I'm also curious about this.Last edited by ben.weisburd; 04-10-2012, 08:56 PM. -
Yes, you are absolutely right. In case of CTX or ITX it reports only two breakpoints(current and earlier position) but it doesn't tell the size of the moved fragment.
Also, in case of insertion event, it reports two breakpoints however I guess there should be only one breakpoint (wrt reference genome) where the another fragment has been inserted.
Any help in this regard will be appreciated.....Comment
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I'm not 100% sure
I'm new to CREST as well, which is actually why I searched this up in the first place. So if someone wants to correct me, please do.
How I've been doing it is looking at the positive/negative strand information. So when it is ITX(which has to either be pn or np (positive-negative/negative-positive), then you look for the nearest of the opposite orientation. So if you see an ITX that is positive-negative, then look downstream for the next ITX that is negative-positive, and that is your length I THINK.Comment
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