01d_Annotation of MAGs with COG profiles - esogin/seagrassOmics GitHub Wiki

Annotation of mags in eggNOG

Created: May 28, 2019

We want to get an idea of the functionality and comparison of bins from different habitats. Goal: from all bins identified as in-edge-out bins, run through the eggNOG mapper to try to get cog profiles. Plot these in a "triangle" space.

Steps:

1. Call prodigal on each bin
2. use eggNOG mapper to map proteins to COG categories
3. Plot!

General script: Need to use python2 to make it work.

cd /path/to/bins/
bins=$(echo ls *fa)
cd /path/to/working/dir/
for i in $bins; 
	do
	# run prodigial 
		prodigal -i bins/$i -o pr_run/genes/${i%%.fa}.faa -a pr_run/proteins/${i%%.fa}.faa;
	# run eggNOG
		cd /scratch/sogin/tmp.$JOB_ID/pr_run/proteins/
		python2 ~/tools/eggnog-mapper/emapper.py -i ${i%%.fa}.faa --output ${i%%.fa}_maNOG -m diamond --usemem --cpu 1;
done