I`m sort of new to this field and I use trinity to assemble my NGS RNA-seq sequences for a fungal species, its genome has not been sequence/annotated. But its sibling species has been fully annotated in genbank. After I got the Tinity output fasta file, I filtered the sequence variants(remove the variants) for faster BLAST2GO annotation.
OK, here is the situation:
After BLAST2GO I have 20301 sequences and only annotated 3334 (just about 15%)of them...
Also, there are 9763 sequences without blast hits...
The N50 is 3784 and the top-hit species is unknown.. which I think it should not...(since the sibling species is very well anotated in the genbank)
There are a number of sequences with seq description simply "gb"....
So The questions are(in your experience):
1, whether using tblastx or blastx will have a effects about the annotation rates?
2, what`s your criteria for the successful annotation rates?
3, how is the seq description "gb" happened.... How could it be replaced by a real name..
OK, here is the situation:
After BLAST2GO I have 20301 sequences and only annotated 3334 (just about 15%)of them...
Also, there are 9763 sequences without blast hits...The N50 is 3784 and the top-hit species is unknown.. which I think it should not...(since the sibling species is very well anotated in the genbank)
There are a number of sequences with seq description simply "gb"....
So The questions are(in your experience):
1, whether using tblastx or blastx will have a effects about the annotation rates?
2, what`s your criteria for the successful annotation rates?
3, how is the seq description "gb" happened.... How could it be replaced by a real name..