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Old 01-09-2014, 11:19 AM   #1
DMD
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Red face Need help with a GenBank submission

Hello everyone,

New to the forum, but I have a question which I hope someone can help me with. I am trying to submit to GenBank Roche 454 16S sequences but is having a small problem. We used the pipeline QIIME for our alignment etc. However, when you submit to GenBank, you need at least the sequence and the organism name. The QIIME pipeline is a bit different. It generates a sequence file and then a phylogeny file which is matched by an identifier. My problem is that I have at least 122,000 sequences. It is nearly impossible for me to perform this manually. This is probably easiest done via a script of some sort (unfortunately I have no script writing ability).

Does anyone know of any open sourced software or of any other programs I could use to resolve this problem. We have already submitted the paper so submitting the sequences is a high priority (I didn't expect it to be this difficult).
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Old 01-09-2014, 11:55 AM   #2
GenoMax
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Should you not be submitting this data via the short read archive (http://www.ncbi.nlm.nih.gov/books/NBK47529/) rather than GenBank (https://www.ncbi.nlm.nih.gov/guide/h...quence-data/)?
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Old 01-09-2014, 12:07 PM   #3
DMD
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Quote:
Originally Posted by GenoMax View Post
Should you not be submitting this data via the short read archive (http://www.ncbi.nlm.nih.gov/books/NBK47529/) rather than GenBank (https://www.ncbi.nlm.nih.gov/guide/h...quence-data/)?
Actually I am. The person at GenBank forwarded my email to SRA. I still need to have the sequences and the phylogeny in the same file as far I know however so I will still need a script or program to do that.
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Old 01-09-2014, 04:46 PM   #4
GenoMax
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Having not submitted similar data I am not 100% sure what exactly it is that you need to do. Can you post an example and the final result you want?

Clearly this problem must have been faced by others before. Nothing seems to come up in searches though.
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Old 01-10-2014, 11:58 AM   #5
cliffbeall
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You can use human metagenome or other metagenome for the taxonomy field in BioSample. Here's some examples we have done, you probably need to tweak things:

http://www.ncbi.nlm.nih.gov/taxonomy/646099
http://www.ncbi.nlm.nih.gov/biosample/?term=SRS379418

P.S. I feel your pain on doing these kinds of submission.
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