James and the Giant Corn Genetics: Studying the Source Code of Nature

April 22, 2012

I/O Limited: Assorted Updates

Filed under: Uncategorized — James @ 1:56 pm

I doubt this will be of interest to that many people but here’s the list of what I’m working on this sunday (each item is a separate project/collaboration):

  • Downloading, decompressing and quality/adapter trimming more than 800 million RNA-seq reads (four full Hiseq 2000 lanes).
  • Attempting to make my very own transcriptome assembly for a species where the genome is available but doesn’t look to be published anytime soon.
  • Figuring out how to look at differential use of exons in maize between male and female floral structures.  (Later on this will involve using some R packages. I’m not looking forward to that part. R always makes me feel like I’m coding with one hand tied behind my back).

The surprising part is that I’m not being held up by a lack of processors to throw at the problem (the usual problem in computation work), nor a limited supply of RAM (probably the biggest problem in bioinformatics specifically). Instead I’m hitting the limit of how fast all these various programs can read data off of hard drives and write results back. Right now I am waiting for a little surplus capacity to free up.

It’s hard to believe that eight months from now this will all be over.  I started my education back in 1990. If they kept numbering years in school after high school I’d be a 20th grader right now. But my adviser has informed me that I need to have graduated by this December, so that’s what I have to make happen. Next week is my last as a graduate student instructor. This summer and part of the fall will be a mad sprint to finish up various projects and collaborations and get them written up for publications, then thesis writing, signing, and submitting are all that stand between me and (hopefully) the last degree I’ll ever need to earn.


  1. Good luck as you finish up. What’s next for you?

    Comment by Noah Fahlgren — April 23, 2012 @ 11:38 am

  2. Thanks Noah!

    I’m still trying to figure out the “what comes next” part. I’d like to stay in comparative genomics and I’m applying for a number of fellowships. Hopefully something works out.

    Comment by James — April 23, 2012 @ 11:57 am

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