Question: refseq NC id list download
0
gravatar for kapil.joshi036
3.2 years ago by
Student ,School of life sciences, Manipal University, Manipal, India
kapil.joshi03680 wrote:

hello i have a list of genes with their nc ids is it posible to download the bulk list from refseq database Thanks

genomics refseq ncbi gene • 1.2k views
ADD COMMENTlink modified 3.2 years ago by genomax68k • written 3.2 years ago by kapil.joshi03680
1
gravatar for ####
3.2 years ago by
####190
####190 wrote:

May be you can try NCBI Entrez http://www.ncbi.nlm.nih.gov/sites/batchentrez

ADD COMMENTlink written 3.2 years ago by ####190

Works pretty well, although with >10,000 entries you might be obliged to split queries (you might get a "bad gateway" error). My longest download consisted of slightly more than 5000 entries.

ADD REPLYlink written 3 months ago by Fabio Marroni2.2k
0
gravatar for genomax
3.2 years ago by
genomax68k
United States
genomax68k wrote:

If you have access to refseq blast databases from NCBI then you can use blastdbcmd to extract the sequence (if that is what you are after).
Other option could be e-utilities from NCBI.

ADD COMMENTlink written 3.2 years ago by genomax68k

Sir, i tried this but its not working for me . any other option to download bulk of NC ids

ADD REPLYlink written 3.2 years ago by kapil.joshi03680

Can you be more specific about what is "not working"? Perhaps we can debug that part.

ADD REPLYlink written 3.2 years ago by genomax68k

I have a list of NC ids of genes of interest , i want to download them into a single shot . so that i dnt need to go for individually download

ADD REPLYlink written 3.2 years ago by kapil.joshi03680

You had already said that in the original post.
The blastdbcmd method should work in this case. If you tried to use that and ran into some problems then let us know what did not work with that method.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by genomax68k
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