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: ...
- 496
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 ...
- 1,739
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 ...
- 1,226
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 ...
- 1,339
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 ...
- 19.5k
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
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, ...
- 189
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 ...
- 1,226
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 ...
- 9,352
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 ?
...
2
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 ...
- 165
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__♦
- 10.2k
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/...
- 152
1
vote
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 ...
- 737
1
vote
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:
...
- 858
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, ...
- 1,226
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 ...
- 66
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__♦
- 10.2k
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