Monday, November 30, 2009

What I learned when I was in Pittsburgh ...

Note: I'm a bit late with this one. Had it 80% of the way written and then forgot about it.

Other than learning that GPS systems are stupid and suck and should never be used, I did learn a few interesting things. I'll relate them here in this post. Some will be rants, some will hopefully be useful bits of information for other people as well (or at the very least drum up a bit of discussion).

1. The American Society of Agronomy is losing members. Hemorrhaging might be the more appropriate word. The society has lost approximately a third of the membership over the last decade, and the trend still points downwards. This is part of the reason that ASA is planning a restructuring which will be coming to a vote probably some time in November.

2. The Cherry Quadzilla at Church Brew Works was awesome. It also only comes in 750ml bottles, so you'll want to take a cab (which we did). Also, bring a camera ... it's a very interesting pub. The chicken pot pie was also really good. As were the perogies.

3. When you are arranging the poster sessions, and you map out where the posters are going to be, discuss the lighting situation with the people at the Convention Center. There was at least one section that after the sun went down and cut out all of the natural light, was in the dark. It was dark enough to hinder reading posters from afar. The rest of the hall was just fine, but at least 40 poster boards were placed underneath an overhang that had absolutely no lighting. That means that approximately 120 people (40 boards over 3 days) had to put up with those cruddy conditions. Unacceptable. I find it hard to believe that after realizing people were sitting in the dark on Monday evening, that something could not have been done to redirect the posters to a better lit area ... which would have required moving some poster boards maybe 40 to 50 feet away. A sign pointing in the direction would have sufficed. The meeting was filled with Ph.D.'s ... if they couldn't handle a redirection of poster boards, they had no job being there anyways.

4. If you plan a business meeting for the 30 minutes before a poster session you are hosting, make sure the business meeting doesn't start with a 45 minute presentation on restructuring. Some of us really had to get to the poster session because we were, you know ... presenting.

5. Metagenomics fraught with pitfalls. I know metagenomics, especially deep 16S sequencing, has taken the microbial ecology world by storm. A whole lot of people have been swept up in the frenzy, including yours truly. Now, I can be a worry wort, and after attending a session where people talked about various metagenomic projects, I just had to go up and ask a question. What about the chimeric sequences? I have a long-ish blog entry on chimeric sequences (which I really need to get out onto the site, it's still a draft), so I won't go into too great a depth on them now, but they're PCR artifacts which can increase your microbial diversity artificially. As pyrosequencing reads get longer, the chances of getting artifacts are probably increasing as well. Any amplification based system is going to have this problem.

So how do you avoid it? Well, I had hoped the people at this session, who have done metagenomic sequencing now for a few years, would have the answers.

None of them did. They figured (rightly, I might add) that the rates would be about the same for these approaches as they would with regular sequencing schemes, but it doesn't help with how to deal with them. Let's do the math.

If you have a 6% chimeric sequence rate (a reasonable value I believe), then you'll have to throw out 6 sequences for every 100 you do. If you have a 200,000 read metagenomic project that's 12,000 sequences you have to throw out. Problem is, how do you find them? Chimera_Check and Bellerophon, the two major programs on the net that do chimera checks, are really hands on programs. You have to really check the results. That's impossible (I won't say near impossible because who is going to read a quarter of a million chimera check reports, other than no one). So what we're seeing is ... no viable (and reliable) way (that I can see) to check metagenomic projects for chimeras. That sucks.

3 comments:

Genomic Repairman said...

Hey can you link up your previous post to chimeric sequences for the general public to read? Also hope you didn't try Iron City as that evil swill is the sweat off of Satan's taint.

Thomas Joseph said...

I haven't posted it yet. I re-read what I wrote and it's a bit deceptive. I'll make the edit, and try to push that other blog entry out ASAP.

soil mama said...

you and I have talked about chimeras a fair amount, and they are a huge problem for bacteria and even more so for fungi. The person I know working on metagenome projects is so wrapped up with the sexyness of the method that these realities of data quality and properly processing the data just don't register. But then again, he wasn't a stickler for details even before metagenomics.
I will have some pyrosequencing data soon myself, then I'll have to make these tough calls!