When at first you don’t succeed…

One of the most frustrating things about science is that you spend a lot of time wondering if you’re headed down the right path. Although having multiple ways of doing things can be a benefit, it can also lead to second-guessing. I have spent more time than I care to admit thinking about whether the method I’m currently using is the best way to achieve results. Unfortunately, the past few weeks have been a lot of trial and error. I spent a week trying to get my data in the correct format in order to use a package on it (PAML; Phylogenetic Analysis by Maximum Likelihood) only to realize that the package wasn’t ideal for the low read coverage data I’m working with. This meant I was forced to jump ship and start trying to figure out a completely new way of doing things.

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Creating the Processing Pipeline

The early stages of my research have been comprised of creating a pipeline of computer scripts that can process the large amounts of genomic data I have. Because the files I’m dealing with are incredibly large (10gb text files) none of the data cleaning and processing can feasibly be done by hand. I’ve tried several strategies to do this, and after weeks worth of failed attempts, I was able to get the major file processed and broken down into much more reasonably sized files that I now have to work on further to fully process to the point where I can use them to create a phylogeny.

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