Week 3: Data Fun

This week we’re moving from the field & lab to computational research…doing 21st century science! (joking…)

We started with the compiled contigs from a Sea Star Transcriptome. Prior to this RNA was extracted – mRNA – 6 libraries were made – compiled seq reads were clustered into contigs using CLC.

Today we got our bearings of the data set using iPython, which allowed us to run commands in the terminal, while simultaneously collecting notes on the commands ran. In addition we were introduced to SQLShare from UW, which allows to compile/join datasets and share datasets as well.

It was a great introduction to the tools and resources out there on the web that we can tool around with (e.g. iPlant). We also learned a few new commands to add to the tool belt:

!fgrep  #faster, but less capable than grep

!awk   #lets you have reports of your data and do data extraction

!sed   #replaces content you don’t want to a new content

 

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