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steineggerlab / ufcg

UFCG: Universal Fungal Core Genes
https://ufcg.steineggerlab.com
GNU General Public License v3.0
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Can you add a new gene in the list and run the whole analysis from profile to tree? #25

Open kusandeep opened 4 months ago

kusandeep commented 4 months ago

Hi, I was just wondering if there is a way to add an extra gene(s)on top of 61 marker genes, in the core gene list before we run the analysis? Thanks, Sandeep

endixk commented 4 months ago

Hi, this is a bit tricky but doable.

First you'll have to generate a model of your custom marker(s) using the train module. You'll need a handful of ground-truth protein sequences as seeds and reference genomes on which the model can be trained.

After this, copy over the resulting .hmm and .fa files to UFCG_PATH/config/model/pro and UFCG_PATH/config/seq/pro, respectively, where UFCG_PATH is your local installation path which can be found by running ufcg download -c.

Then, generate a comma-separated string that includes the names your custom gene(s) and 61 marker genes (e.g. GENE1,GENE2,...,ACT1,ATP6,...,ZPR1), and pass this string via -s flag of the profile module. This will allow you to extract your extra gene(s) on top of the original marker genes.

These may sound confusing and tedious, which I apologize, so please let me know if you have any further questions or encounter any problems following the procedure.