Hi folks, I produced a chromosome-level plant genome assembly and accompanying annotation in gff format. I am running NCBI's table2asn (https://www.ncbi.nlm.nih.gov/genbank/table2asn/) to convert the gff annotation to the NCBI format so that I can upload it to NCBI along with my genome. I am getting the error message "SEQ_INST.SeqGapProblem: 8" in my .stats output file (I have 8 chromosomes). When I look in the .val output file, it specifies, "Genome submission includes wrong gap type. Gaps for genomes should be Assembly Gaps with linkage evidence". My genome assembly's gaps were generated by the Juicebox Assembly Tools pipeline using HiC data evidence-- that pipeline adds a gap of fixed size (500bp) in between each pair of input scaffolds in its finalization step (https://aidenlab.org/assembly/manual_180322.pdf). Does anyone know how I can indicate that to the table2asn software?
(This is my first Biostars post so let me know if I need to fix anything!) Thanks!!
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