I am new to antismash analysis and using the updated/latest version 5.0 therefore can not find answer of my questions in the older threads.
Here is the detail:
I ran antismash and obtained .gbk files as well as a new folder called "region1". (I belie this is the new thing in the latet version). This folder contains several .html files that look like this "ctg3_14_mibig_hits.html" and so on....
When I open this .html file, it contains the following eight columns:
- MIBiG Protein
- MIBiG Cluster
- MiBiG Product
- % ID
- % Coverage
- BLAST Score
The fourth column (MiBiG Product) contains name of the product e.g. NRP, polyketde, tarpene, other etc. and I am interested in counting the number of BGCs types in each sample. (may be from this column?)
Q1. I am confused which file should I use to count the BGC types? This .html file (I have several) under the "region1" folder or .gbk file?
Q2. In either case, I need a method/script to do so. I will really appreciate if someone can please share the code/script for counting the BGCs in each sample since I have several such files and then tens/hundreds of MIBiG product in each file.
Please help this newbie.