This is a test version of Biostars. For the public version, visit https://www.biostars.org.
PSL file confusion on negative strand

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:

Track uploaded to Genome Browser

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?

blat psl

0 answers

No answers yet.

Log in to answer this question.