Catching up....
I can't believe it's been nearly a month since my last post! I feel like I've been neglecting this a bit more than I should, but I'll try to rectify that as best I can.
For an indication of how busy I've been, I sat down to update my resume yesterday, and ended up adding 3 papers (all in submission) and two posters. That just about doubles what was in there previously in the papers section.
Anyhow, Next-generation sequencing doesn't stand still, so I thought I'd outline some of the things I want to talk about in my next posts, and set up a few pointers to other resources:
1. SeqAnswers. This aptly named forum has been around for a few months now, but has recently become more popular, and a great forum for discussing relevant Next-gen technology and sequencing methods. I'm especially happy to see the automated posts triggered by new literature on the subject, which are a great resource for those of us who are busy and forget to check for new publications ourselves.
2. There's one forum in particular that's of great interest: Benchmarking different aligners. This appears to be a well done comparison (if lightweight) that may be a good focus for other people who are interested in comparing aligners, and discussing it in a wider forum.
3. For people interested in ChIP-Seq, or Chromatin immunoprecipitation and massively parallel sequencing, I've finally gotten around to posting FindPeaks 3.1 on the web. I'd consider this release (3.1.3) an alpha release. I'd love to get more people contributing by using this application and telling me what could be improved on it, or what enhancements they'd like to see. I'm always happy to discuss new features, and can probably add most of them in with a relatively quick turn around time.
4. For people interested in assessing the quality of the whole transcriptome shotgun sequencing (WTSS), I'm about to break out a tool that should fit that purpose. If anyone is interested in giving suggestions on ways they'd like to see quality tests performed, I'd be more than happy to code those into my applications. (And yes, if you contribute to the tool, I will provide you a copy of the tool to use. Collaborations, etc, can be discussed, as well.)
5. A quick question, of which I'll post more in the future. Has anyone here managed to get Exonerate 2.0 to work in client/server mode on two separate machines?
6. I'll also post a little more about this in the future: building environments, ant and java. Why are people still doing large projects in perl?
7. One last thing I wanted to mention. I was going to write more on this topic, but eh... I'll let slashdot do it for me: The more you drink, the less you publish. Well, So much for keeping a bottle of tequila under the desk. Now I know what to get the competition for x-mas, though...
Cheers!
For an indication of how busy I've been, I sat down to update my resume yesterday, and ended up adding 3 papers (all in submission) and two posters. That just about doubles what was in there previously in the papers section.
Anyhow, Next-generation sequencing doesn't stand still, so I thought I'd outline some of the things I want to talk about in my next posts, and set up a few pointers to other resources:
1. SeqAnswers. This aptly named forum has been around for a few months now, but has recently become more popular, and a great forum for discussing relevant Next-gen technology and sequencing methods. I'm especially happy to see the automated posts triggered by new literature on the subject, which are a great resource for those of us who are busy and forget to check for new publications ourselves.
2. There's one forum in particular that's of great interest: Benchmarking different aligners. This appears to be a well done comparison (if lightweight) that may be a good focus for other people who are interested in comparing aligners, and discussing it in a wider forum.
3. For people interested in ChIP-Seq, or Chromatin immunoprecipitation and massively parallel sequencing, I've finally gotten around to posting FindPeaks 3.1 on the web. I'd consider this release (3.1.3) an alpha release. I'd love to get more people contributing by using this application and telling me what could be improved on it, or what enhancements they'd like to see. I'm always happy to discuss new features, and can probably add most of them in with a relatively quick turn around time.
4. For people interested in assessing the quality of the whole transcriptome shotgun sequencing (WTSS), I'm about to break out a tool that should fit that purpose. If anyone is interested in giving suggestions on ways they'd like to see quality tests performed, I'd be more than happy to code those into my applications. (And yes, if you contribute to the tool, I will provide you a copy of the tool to use. Collaborations, etc, can be discussed, as well.)
5. A quick question, of which I'll post more in the future. Has anyone here managed to get Exonerate 2.0 to work in client/server mode on two separate machines?
6. I'll also post a little more about this in the future: building environments, ant and java. Why are people still doing large projects in perl?
7. One last thing I wanted to mention. I was going to write more on this topic, but eh... I'll let slashdot do it for me: The more you drink, the less you publish. Well, So much for keeping a bottle of tequila under the desk. Now I know what to get the competition for x-mas, though...
Cheers!
Labels: Aligners, Code planning, Sequencing, Solexa/Illumina
2 Comments:
HI, Nice blog; one question - what kind of computing infrastructure do you need to be able to handle chipSEQ datasets? I'm guessing my standard IBM T60 laptop is not going to do the trick - but what does?
Can't believe I haven't kept a closer eye on my referrers until now!
Thanks for the props...much of the popularity is due to your insight and great posts.
Thanks again...
-=Eric@SEQanswers
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