https://www.biostars.org/p/44633/ In general the coordinates in psl files are “zero based half open.” The first base in a sequence is numbered zero rather than one. When representing a range the end coordinate is not included in the range. Thus the first 100 bases of a sequence are represented as 0-100, and the second 100 bases are represented as 100-200. There is a another little unusual feature in the .psl format. It has to do with how coordinates are handled on the negative strand. In the qStart/qEnd fields the coordinates are where it matches from the point of view of the forward strand (even when the match is on the reverse strand). However on the qStarts[] list, the coordinates are reversed. Here's an example of a 30-mer that has 2 blocks that align on the minus strand and 2 blocks on the plus strand (this sort of stuff happens in real life in response to assembly errors sometimes). 0 1 2 3 tens position in query 0123456789012345678901234567890 ones position in query ++++ +++++ plus strand alignment on query -------- ---------- minus strand alignment on query Plus strand: qStart 12 qEnd 31 blockSizes 4,5 qStarts 12,26 Minus strand: qStart 4 qEnd 26 blockSizes 10,8 qStarts 5,19 Essentially the minus strand blockSizes and qStarts are what you would get if you reverse complemented the query. However the qStart and qEnd are non-reversed. To get from one to the other: qStart = qSize - revQEnd qEnd = qSize - revQStart
标签: alignment
