New ChIP-Seq tool from Illumina
Ok, I had to blog this. Someone on the SeqAnswers forum brought it to my attention that Illumina has a new tool for ChIP-Seq experiments. That in itself doesn't bother me - the more people in this space, the faster we learn about what makes us tick.
What surprises me, though, is the tool itself (beadstudio data analysis software - chip sequencing module). It's implemented only for Windows, for one. (Don't most self-respecting scientists use Macs or Linux these days? Or at least use and develop tools that can be used cross-platform?) Second, the feature set appears to be a re-implementation of the UCSC Genome Browser. Given the choice between the two, I don't see any reason to buy the Illumina version. (Yes, you have to pay for it, whereas UCSC is free and flexible.) I can't tell if it loads bed files or wig files, but the screen shots show a rather unflexible tool that looks like a graphical version of Gap4 or Consed. I'm not particularly impressed.
Worse still, I can't see this being implemented in a pipeline. If you're processing 100's of ChIP-Seq experiments in a year, or 1000's once this technique really starts to hit it's stride, why would you want to force it all through a GUI? I just don't get it.
Well, what do I know? Maybe there's a big market for people out there who don't want free cross-platform tools, and would rather pay for a brand name science application than use something that works. Come to think of it, I'm willing to bet there are a few pharma companies out there who do think like that, and Illumina is likely to conquer that market with their tool. Happy clicking, Vista users.
What surprises me, though, is the tool itself (beadstudio data analysis software - chip sequencing module). It's implemented only for Windows, for one. (Don't most self-respecting scientists use Macs or Linux these days? Or at least use and develop tools that can be used cross-platform?) Second, the feature set appears to be a re-implementation of the UCSC Genome Browser. Given the choice between the two, I don't see any reason to buy the Illumina version. (Yes, you have to pay for it, whereas UCSC is free and flexible.) I can't tell if it loads bed files or wig files, but the screen shots show a rather unflexible tool that looks like a graphical version of Gap4 or Consed. I'm not particularly impressed.
Worse still, I can't see this being implemented in a pipeline. If you're processing 100's of ChIP-Seq experiments in a year, or 1000's once this technique really starts to hit it's stride, why would you want to force it all through a GUI? I just don't get it.
Well, what do I know? Maybe there's a big market for people out there who don't want free cross-platform tools, and would rather pay for a brand name science application than use something that works. Come to think of it, I'm willing to bet there are a few pharma companies out there who do think like that, and Illumina is likely to conquer that market with their tool. Happy clicking, Vista users.
Labels: Chip-Seq, Software, Solexa/Illumina
1 Comments:
Hey Eco - thanks for the comments. I've deleted both, as per your request.
And yes, there are lots of links back to seqanswers - I certainly get a lot of hits coming from your pages as well, so I hope I can return the favour.
By the way, It'll probably be another 2 years minimum till I graduate. Hopefully some of those good jobs will still be around!
Anthony
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