Differences of BUSCO results on different levels
Hello,
I sequenced and annotated an ant genome. So, I ran BUSCO on genome,transcript, and protein level with OrthoDB v.9 (Hymenoptera subset):
Genome: C:95.8%[S:93.6%,D:2.2%],F:3.3%,M:0.9%,n:4415 --> 41 Missing BUSCOs (M) Transcripts: C:91.6%[S:81.0%,D:10.6%],F:5.2%,M:3.2%,n:4415 --> 142 Missing BUSCOs (M) Proteins: C:90.5%[S:83.4%,D:7.1%],F:5.9%,M:3.6%,n:4415 --> 158 Missing BUSCOs (M)
Unfortunately I am missing some genes from the genome to the transcript level, which may be because of missing tissues from transcript experiment. What surprises me is the difference in missing genes between transcripts and proteins. As I submitted the transcripts which are coding for the proteins, I would expect the same number of missing BUSCO's in the result.
I guess maybe it depends on the different detection strategy or on the definition, when a BUSCO gene is a missing gene?
I am looking forward to your reply.
Best regards, Jonas