Hi @lastewart ,
You could check NCBI GenBank for 12S seqs for birds. If it is sufficient enough, then RESCRIPt would be a good solution. See some examples here for making (non-bird) 12S databases with RESCRIPt:
Hi @Junli_Zhang ,
I’ve got quite a bit of experience in making 12S rRNA gene databases (e.g. for eukaryota, and metazoa). Hopefully, we can help. @Nicholas_Bokulich , there are things beyond our control when it comes to internet connections. Your query does not appear to result in that many sequences, but you can break it up into smaller downloadable chunks within the vertebrates.
Here is a query you can use to download Gnathostomata:
txid7776[ORGN] AND (12S OR 12S…
Hi there,
I've been using and loving rescript for my eDNA metabarcoding projects. I was wondering if it was possible to filter sequences returned from NCBI before downloading them.
For example, I'm doing a metabarcoding project using the 12S gene targeting fishes. One of the target species Percina brevicauda (txid163812) has its entire mitochondrial genome sequenced, but does not have individual entries for just the 12S gene. If I were to use this search, I would not get any results:
qiime re…
You can check GenBank first to test out a query and see how many hits you get.
Good luck!