Entering edit mode
5.7 years ago
popayekid55 ▴ 110
I have submitted one bacterial genome (single Contig from nanopore and illumina data) to ncbi. Ncbi has sent set of coordinates saying adapter contamination. Extracted sequences from those coordinates and checked for adapter (QXT kit) and found no occurence. Also checked these sequences against ncbi NR and they are showing homology for B. Coagulan which is the nearest reference.
Any suggestions to resolve this ??
Thank you all
What is their reasoning behind it? I would recommend keep writing emails to folks at ncbi. They are pretty responsive. You can provide this evidence that it is not contamination.
This has been done. Awaiting their response. Any other insight to look at the problem. Is there any way I run through the genome in ncbi pipeline before submission ??
Are you sure you do not have contamination from other adapter, not from your kit?
What are your re-alignment values, i.e., when you realign your samples to the new genome that they were used to create?
It looks like you have already assured yourself that there is no contamination. Why not send your evidence back to the NCBI? Maybe they made an error - we are all prone to making errors at any level and age, or perhaps they saw homology to B. coagulan and did not realise that that it's a close relative.
NCBI is saying that there is adapter contamination with what looks like Sureselect whole genome library prep kit adapters. It should be easy enough to extract the area in question and see if it aligns with the adapters. If the evidence is negative then it can be sent in to NCBI.