I got DAVID working!

After hours spent working out erroneous scripts of course. I had a bright idea to rerun DESeq2 in an effort to compare transcriptomes from 2 out of the 3 sites where we collected our sea stars to see if immune response changes in stars with different exposure histories, but kept running into problems with scripts, R codes, and file jumbling. The good news is my scripting tool belt is definitely expanding.

After cleaning up my database files and retracing my database libraries, I decided to take another shot at joining our differentiated transcriptome with spIDs and loading onto DAVID for bioinformatics analysis. I had a much easier time getting to DAVID and running my DESeq contigs against the Phel database and got some fun pathways up on the screen. Next up, ReviGO!

I’ll post my IPython notebook as soon as they’re loaded onto lilmax.

Update: Here I am cleaning up house:

….and here I am attempting to compare site effects:

Had a great time at the speed talks tonight! EIMD covered a lot of ground…. paleobiology, algal phycology, fly genetics and behavior, and coral disease.

Leave a Reply