Notebook notebook

In which I explore read alignments in SAM format and discuss the pros and cons of various approaches to distinguishing perfect matches from imperfect matches.

In which I briefly motivate the utility of generator functions and demonstrate that they can be nested to create a data processing stream.

I created a table for my iLocus paper tonight, and wanted to capture the commands used to populate it while everything is still fresh in my mind.

Some notes on my data forensics to determine whether there are any differences between the RefSeq Arabidopsis annotation and TAIR10.

I gave another group meeting today, this time on random arrangements of iLoci. This entry records feedback I received from the group members.

I recently sketched out some notes on random placement of genomic intervals. Here I show a more concrete implementation

I've been looking at statistics of gene spacing, but as of yet have not compared these to benchmarks of "randomly" distributed genes. Here I sketch out a few rough notes on the topic.

Today I had the privilege of attending an excellent departmental seminar from an invited speaker. I've seen plenty of great seminars in grad school but I've also experienced my fair share of seminars that were...less than phenomenal. The content of the talk was interesting, and the speaker's presentation was engaging, but there were a couple of things on top …

I gave a group meeting today on my iLocus work, and got some good feedback from the group.

We submitted a genome paper to Genome Biology over the weekend. I'm going through our repository and tidying things up, and I realized I have not had a chance to record my notes on several of the supplemental tables providing a comparison of genome features across seven species. I'll go ahead and do so here.