Entering edit mode
21 months ago
spark
•
0
Hello, I have some confusions on PSL file format. The UCSC website says:
Essentially, the minus strand blockSizes and qStarts are what you would get if you reverse-complemented the query. However, the qStart and qEnd are not reversed.
However, when I upload this track to the Genome Browser,
6792 0 0 0 0 0 12 94868 - m2970183067:f1511127721 6792 0 6792 chr22 50818468 35738756 35840416 13 5493,73,89,43,145,93,54,61,93,54,144,225,225, 0,5493,5566,5655,5698,5843,5936,5990,6051,6144,6198,6342,6567, 35738756,35745922,35746472,35752612,35759887,35761201,35761414,35765422,35768256,35778024,35781599,35809779,35840191,
This is the result:
To my knowledge, if the blocksizes and qStarts are reversed, the last block supposed to be the longest one (blockSize 5493). However, in the image above, the first block is the longest one.
Would anyone know where this confusion comes from?