Postdoc Diary: Day 24 - LD overload

I woke up this morning around 7 and headed downstairs to get the morning cup of coffee, then get ready to go to work. Got geared up and headed out a little bit later than I wished. Got to work and wrote out the to-do list. Not that different than today. I have to get motivated to write the discussion. Probably I will do the references then go in and finish the paper.

1. Discussion and Conclusion (mtDNA)
2. References (mtDNA)
3. Chrm 9 Hrt Rate

• Run QTLD (AZ, All)
• SNP LD by gene for OK
  

4. MAPP data

• Run polygenic screen on remaining sixteen variables
• Run bivariate on remaining sixteen variables
• Run trivariate on Visits 1 and 3 and differences
  

5. Clean Home office

I get to work on looking at the trivariate differences and notice that the .tcl script is on the wrong chromosome so I go ahead an modify that. The only drawback to this technique is that it takes a long time. I check the QTLD for AZ and ALL and that is still running. Wow, this is taking a long time but still not as long as the linkage screen I did that took a month and another person I know has been running a linkage screen since Dec. 15th, so there is a tremendous amount of computing power sucked up by this. I then start doing the LD by gene for OK, so get that working - there are a number of step involved in this. First create a map, then load the file, then compute the maximum likelihood frequencies of the SNPs, then convert these to 0,1, and 2s so they can be computed. This takes most of the morning, I do a little work on the discussion. I hate writers block so I do a few other things. I outline the discussion a little more, I think because I take so much time on the discussion, it slows things down. I'm also co-author on presentation at KU tomorrow, so I do an on-line chat with him. We talk a little about a disease called grisi skinis that only affects the Miskito of the Caribbean and seems to be pronounced along the Rio Coco between Honduras and Nicaragua. He is headed to the field this summer to collect some more samples for his dissertation. Got that done and he sent me some questions, which I answered. By this time it is almost time to go home. I finish up the LD for another gene, and check the other two things and gear up to go home.

I get home, we're having hot dogs. Then I run through the normal night time schedule for the kids, X gets his bath, then S and C hop in, then hot milk, then a little play time, then story time, then time for C bed time. After that X and I play a little Rock commando game, then I read X Harry Potter and I put him to sleep. S has come downstairs to watch Chopped with J and L. So I head down and play on the computer. I'm trying to copy a DVD to play on any type of player. I figure that out and then head up to bed with J and L. Today's progress was slow, hopefully we can pick up the pace tomorrow.