Why # predicted genes is -1?

[B-1991-ing]

Hi Matt,

Why in my Chdb.csv, the column - "# predicted genes" is -1?

Chdb.csv

Best,

Bing

[MrOlm]

Hi Bing,

dRep calls genes on its own using Prodigal and then provides those genes to checkM. I guess checkM reports the number of genes as -1 when you do this.

Best, Matt

[B-1991-ing]

Hi Matt,

Can I directly know how many predicted genes in each MAG from the drep output file as shown in the screenshot?

Best,

Bing

[MrOlm]

Hi Bing,

You'll have to calculate this information manually. In the data/prodigal folder you should see the gene files for each genome. You could could the number of genes in each file using a program for that purpose or a linux command like cat file | grep '>' | wc -l

Best,
Matt

[B-1991-ing]

Thank you very much for your reply, Matt.

I just calculated the prodigal-predicted genes in my MAGs as you suggest.

Best,

Bing

[MrOlm]

Great! Glad I could be of help