Hot answers tagged

6 votes

How to obtain NCBI Nucleotide (Entrez) IDs for all E coli sequences?

Do you mean the NCBI taxonomy IDs? If so, I've personally always preferred the way UniProt displays NCBI taxonomy, and it's easier to download IDs in mass. For example, if you find E.coli's entry: ...
Bioinfomrat's user avatar
5 votes

Why the gene symbol aliases have significantly different sequences?

At Ensembl, we categorise synonyms as anything that a gene might also be known as. This includes older names for them, since those names will be in the literature, including where a gene has been ...
Emily_Ensembl's user avatar
5 votes
Accepted

Entrez.efetch returns incomplete genbank records

This has been answered before. See: https://stackoverflow.com/a/55402322/6262370 In short, you need to either use rettype='gbwithparts' or ...
vkkodali's user avatar
  • 1,266
4 votes

How to identify which isoforms of a gene are actually expressed in my data?

Tools like kallisto or salmon can perform a process call pseudo-alignment that matches reads from RNA-seq data to transcript isoforms present in a reference genome. You can then look at the output of ...
James Hawley's user avatar
  • 1,384
3 votes
Accepted

Getting ALL Protein entries from Entrez for a particular taxonomic id

As suggested by somebody, the datasets tools from NCBI is blazing fast: datasets download genome taxon 187492 --include protein NCBI Datasets Tool
The August's user avatar
3 votes

How to identify which isoforms of a gene are actually expressed in my data?

If you do as @james-hawley rightly suggests, keep in mind that pseudo-alignment could detect a lot of transcripts with low TPM that are actually false positives, as reported here (it's a paper ...
bepoli's user avatar
  • 175
3 votes
Accepted

Why doesn't an (Entrez eutils) einfo request for "gene" return the link gene_nucleotide or gene_nucleotide_pos links?

I've been corresponding with NLM about this issue and I finally took the time to try out their suggestion (which personally I found hard to see between the lines and which is not a discrete solution, ...
hepcat72's user avatar
  • 221
3 votes

How to extract metadata from NCBI's experiment?

You'll want something like: esearch -db sra -query SRX1596422 | efetch -format runinfo This will produce a CSV output to the screen with columns containing the ...
Devon Ryan's user avatar
  • 19.6k
2 votes

Why the gene symbol aliases have significantly different sequences?

Answer from @devon-ryan, converted from comment: Both, that's why NAT5 is no longer a human gene symbol. NAT5 does not equal NAA20, it's an out-dated name for it. Names change over time as people ...
2 votes
Accepted

Using Entrez.efetch() to retrive .fasta file from any NCBI database?

In order to download the FASTA sequence of transcript variants using Entrez eutilities, you will have to use Entrez.elink to get a list of transcript accessions for ...
vkkodali's user avatar
  • 1,266
2 votes

curl: (22) The requested URL returned error: 400 Bad Request when using entrez direct

It's not a curl problem. (The 22 error is just passing along the server-side HTTP 400 error, which is because it dumped an error message into a URL.) I think terdon is right and there's something ...
Jesse's user avatar
  • 947
2 votes
Accepted

Convert Entrez gene ids and HUGO symbols, whose genome assembly is unknown, to GRCh38 Ensembl gene ids

Hugo names don't really have an associated assembly. They are just the official name of the gene in human. You will find them in all assemblies (except if they hadn't been annotated/identified in one ...
terdon's user avatar
  • 9,846
2 votes
Accepted

Entrez (Biopython) esearch and efetch not returning sequence as expected

Did you try to fetch from the database nucleotide instead of gene ? ...
Pierre-Edouard Guerin's user avatar
1 vote
Accepted

How to set Entrez Direct - ESearch NCBI entrez to pipe or ignore errors?

This is because there are not assemblies for Crepis commutate within NCBI's assembly database. The cross check is here: https://www.ncbi.nlm.nih.gov/assembly/?term=Crepis+commutata The output is a bit ...
M__'s user avatar
  • 12.1k
1 vote

Is there an equivalent of Entrez queries for local BLAST?

I looked back at the question and have a more comprehensive solution. There is no option for -entrez_query on a local blast search. The information is here ...
M__'s user avatar
  • 12.1k
1 vote

Getting translation table of organisms through Entrez direct (or other CLIs)

I came up with this idea. So, the information for the translation table of any particular organism can be found on its page on the Taxonomy Browser: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/...
arara's user avatar
  • 152
1 vote

Long-form gene summary

The following bash script downloads the summaries into an XML file. ...
user66081's user avatar
  • 151
1 vote

Long-form gene summary

You could wrap the call too entrez_summary in a loop. For example to cut the data into chunks of five genes: ...
PPK's user avatar
  • 886
1 vote
Accepted

How to obtain NCBI Nucleotide (Entrez) IDs for all E coli sequences?

You should check out NCBI Datasets for this sort of thing. Since this is bacteria, you won't be able to use the web interface but there's an API and a command-line tool that you can use. For example, ...
vkkodali's user avatar
  • 1,266
1 vote

Finding annotated counterpart after BLASTn with efetch (Biopython)

Lets assume you can get the blastn output in a BED format: ...
darked89's user avatar
  • 273
1 vote

Finding annotated counterpart after BLASTn with efetch (Biopython)

It seems like the seq_start and seq_end are sensitive to the direction. Try swapping the two.
RaphiS's user avatar
  • 11
1 vote
Accepted

How to query NCBI (Nucleotide database) by a feature qualifier?

For this particular query, try host=Bemisia tabaci B[WORD]. However, you may also be interested in related queries like host=Bemisia tabaci B biotype[WORD]. But, I am not sure a general solution ...
Brad Holmes's user avatar
1 vote

rentrez to retrieve NIH files

I don't program in R, but replace the last line of you code with the following and I suspect you will find it works, ...
M__'s user avatar
  • 12.1k

Only top scored, non community-wiki answers of a minimum length are eligible