Entering edit mode
10.4 years ago
chae
▴
40
I have probe set sequence files in fasta format which are download from affymetrix or agilent. But some are built against hg18 and others are based on hg19 reference genome. Here, I'd like to make or change all sequence files in fasta format against hg19 reference.
What should I do? I guess there may be several ways to do it. The simpler will be the better.
Sequence for a probe should remain same between different versions of human genome. It is their location that varies between different versions. Sometimes the sequence gets updated too in case there was an error in the previous reference genome itself but it doesn't happen frequently. So, I don't think you need to convert the sequences.
I agree with ashutoshmits. A conversion of sequences is not beneficial and an attempt would be misguided. Keep in mind that the probe sequences correspond to real sequences on the chip, and these did not change. Possibly, the annotation of probe-sets and their genomic coordinates could have changed, but that is a different story.
You may use liftover to update the coordinates against hg19.
http://genome.ucsc.edu/cgi-bin/hgLiftOver