We have sequenced a eukaryotic genome (~32Mb size) and submitted the assembly sequences (chromosomes) to NCBI. Now while performing annotation of the assembly, first we used MAKER to generate gff3 file of the chromosome. Next, to generate .SQN file (for submitting the annotation to NCBI), we used NCBI Genome Workbench software. The Genome Workbench generates .SQN file, but it does not incorporate the features (i.e., genes, cds, exon etc. from the gff3 file) into the resultant SQN file, resulting in a malformed or annotation-less SQN file.
Can anyone please suggest the possible reason and solution of it.
Thanks
•
written
by
SAsciences •
1 answer
Hi
Recently, I used https://www.gensas.org/ to make the annotation. It was pretty practical and in my opinion easy. You just need to upload your genome an some evidence from RNAseq or protein. It executes different approaches for structural and functional annotation that you can filter at the end .
Log in to answer this question.
-
NCBI Genome Workbench Sequence ID edit
written by Paige •
-
MAKER: how to use RNAseq data to assist annotation?
written by bbscience •
-
Mapping RNA-Seq reads onto viral genome
written by nik.kraemer •
-
GenCodeMismatch in .sqn file, is there any solution?
written by Buffo
-
Changing gene headers in .sqn file for genome upload NCBI
written by T_18 •
-
GenSAS merged annotation GFF3 file to NCBI .sqn file for NCBI genome submission
written by zack.saud •
-
High CDS Count in my assembled Genome using Nanopore reads (ONT) data
written by Optimist
-
Issue wiht pseudogenes in bacteria genome
written by hjafar •
-
Differences in annotations using Prokka on assembly done by SPAdes
written by jeetsahu •
-
start codon gff annotation corrections using fasta file
written by rob234king
