drep icon indicating copy to clipboard operation
drep copied to clipboard

Published 20 hours ago • verified publisher icon MrOlm

Why the value of # scaffolds, # contigs, and Predicted genes are same?

Open B-1991-ing opened this issue 2 years ago • 2 comments

Hi Matt,

Screenshot 2022-08-31 at 10 41 13

The column of # Schaffolds in my Chdb.csv file and my Predicted genes are the same. What went wrong there according to your experience?

Best,

Bing

B-1991-ing avatar Aug 31 '22 08:08 B-1991-ing

Hi Bing,

DRep provides checkM with genes, not scaffolds, so checkM has no way to know the correct number of scaffolds in a genome.

The number of genes is probably correct, number of scaffolds is incorrect

-Matt

MrOlm avatar Aug 31 '22 15:08 MrOlm

Thanks for your confirmation, Matt.

I self-checked the number of scaffolds, GC, predicted genes using script.

B-1991-ing avatar Aug 31 '22 15:08 B-1991-ing