tag:blogger.com,1999:blog-36768584.post5977196212741800260..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Version Control FailureKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-36768584.post-40925967998092089152010-04-12T13:52:10.473-04:002010-04-12T13:52:10.473-04:00I had a similar experience when trying to replicat...I had a similar experience when trying to replicate other people's work. I found that http://genome.ucsc.edu/cgi-bin/hgLiftOver is a pretty good tool.Weihttps://www.blogger.com/profile/04410901364184832690noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-2274361078288599382010-04-09T13:51:00.892-04:002010-04-09T13:51:00.892-04:00My understanding is that agilent's hg19 versio...My understanding is that agilent's hg19 version of probes is much more efficient, and they wish to use that for a better comparison!<br /><br />I agree with the public datasets. Its really hard to go from one of these nextGen papers to their data!smhttp://kromozome.wordpress.com/noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-39793851911590481872010-04-08T14:53:04.725-04:002010-04-08T14:53:04.725-04:00I'm not sure I follow.
I'm fairly confide...I'm not sure I follow.<br /><br />I'm fairly confident they did not upload hg19 genomic intervals into Agilent's system. I've done that myself and it led to complete junk, I'm extremely skeptical doing that would yield 70% coverage as reported in the article.<br /><br />What seems more likely is that they took probes designed for hg19 and BLASTed them against the hg18 genome. That will mess up the spacing of probes a little, but agilent claiming that it alone accounts for the lack of coverage seems a little suspicious to me.<br /><br />But yeah, either way, it's very sloppy work, and without actual study we can only speculate.bishnuhttps://www.blogger.com/profile/13724998703214594527noreply@blogger.com