Grace’s Notebook: BLAST on Hummingbird and Transrate

Today I attempted to take my BLAST output on Hummingbird and work through this blast-2-slim notebook of Steven’s. I had gone through this before using Cgigas. I got stuck today at the part where you !join _blast-GO-unfolded.sorted with GO-GOslim.sorted. Will ask tomorrow. Additionally, today I worked on using transrate to look at my C. bairdi assembly using Laura’s notebook as a guide.

BLAST to GO slim

The notebook is in the Downloads on Hummingbird in grace-Cbairdi-transcriptome/notebooks/20181105-blast-Cbairdi_swiss-prot.ipynb. I couldn’t figure out how to commit and push it successfully to my GitHub repo notebook… but I rsync-ed the notebook to Owl from Hummingbird: /scaphapoda/grace/Crab-project/20181025-blast-Cbairdi_swiss-prot.ipynb.

Anyway, I got stuck where you have to !join the _blast-GO-unfolded.sortedwith GO-GOslim.sorted. I checked the two files in TextWrangler on Hummingbird, and they both looked good. Additionally, I looked at the files using !head and !tail. The one thing that I noticed, which I’m not sure is typical, is that in the _blast-GO-unfolded.sorted file, there were a lot more rows of the “TRINITY_DN#…” column, than there where of the “GO….” column. Maybe that is the problem?

Will ask Steven or Sam tomorrow morning.


I used Transrate today and followed Laura’s notebook. Here’s my notebook post: Cbairdi_01_tranrate.ipynb. I’m not sure what else I should do with this, so I’ll ask tomororw.


This Thursday is GSS. I’m hoping to have some basic assembly data to share on my poster, and I’ll have some stuff after I get the above issues sorted out.

from Grace’s Lab Notebook