Questions tagged [entrez]
The entrez tag has no usage guidance.
22
questions
2
votes
1
answer
41
views
Getting ALL Protein entries from Entrez for a particular taxonomic id
I'm trying to get ALL Proteins for a Taxonomic ID from Entrez using Esearch/Efetch and the following command:
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- 203
2
votes
0
answers
58
views
Get SRR numbers from a GSE number
I'm trying to programmatically download files from SRA (with prefetch in sra-tools) starting from a GSE number, using Python.
There is an explanation for using entrez-direct on the CLI, using esearch ...
- 563
1
vote
1
answer
105
views
How to set Entrez Direct - ESearch NCBI entrez to pipe or ignore errors?
I am using the following one-liner with NCBI entrez to query their databases from the terminal (see Entrez Direct: E-utilities on the Unix Command Line:
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- 217
2
votes
1
answer
37
views
How to find specific types of assemblies for specific species using entrez tools?
How to find specific types of assemblies for specific species using entrez tools?
Task: Trying to specifically find transcriptomes and associated cDNA data for a list of speices.
I can use this ...
- 217
1
vote
2
answers
132
views
Is there an equivalent of Entrez queries for local BLAST?
I have been having some trouble with running command line BLASTn remotely. Therefore, upon recommendations, and considering I have >100 searches planned, I am considering just downloading the nt ...
- 881
2
votes
2
answers
392
views
How to identify which isoforms of a gene are actually expressed in my data?
I am new to bioinformatics and have been assigned the task of discovering which isoforms of a certain protein-coding gene are present in the RNA-seq data that I have. There are several isoforms of ...
- 21
0
votes
0
answers
1k
views
Converting Gene Symbol to Entrez ID in R
I analyzed a GEO dataset and found 99 DEG.Now I want to analyze functional enrichment analysis and for that reason I have to convert my gene symbol to entrez id.But I cannot do that,I tried but my ...
1
vote
0
answers
25
views
Download COX1 (COI) gene via biopython using accessions for entire mitochondrial genomes
I have a list of accessions for the the entire mitochondrial genomes for big cats. I need to download the COX1 genes for each of these accessions.
Here is one accession and here is a link to its COX1 ...
- 131
1
vote
2
answers
75
views
Getting translation table of organisms through Entrez direct (or other CLIs)
I have a long list of NCBI taxonomic ids for organisms and I want to write a script to get their corresponding translation tables. Is there a way to do this through Entrez?
(packages in R, Python etc. ...
- 11
0
votes
1
answer
11k
views
curl: (22) The requested URL returned error: 400 Bad Request when using entrez direct
I've just dowloaded entrez direct on my Mac and I was trying to perform some simple queries like:
...
1
vote
1
answer
1k
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Convert Entrez gene ids and HUGO symbols, whose genome assembly is unknown, to GRCh38 Ensembl gene ids
I want to use a file available on a database called DepMap (https://depmap.org/portal/download/). This file called ...
- 665
2
votes
1
answer
475
views
Entrez (Biopython) esearch and efetch not returning sequence as expected
I'm trying to use Entrez (through Biopython) to download the sequence of a TMV replicase gene.
I have the following code:
...
- 23
1
vote
2
answers
55
views
Long-form gene summary
The following
(thx to these answers)
retrieves the info, in particular a long summary (such as "The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding ...
- 151
0
votes
1
answer
1k
views
Using Entrez.efetch() to retrive .fasta file from any NCBI database?
I tried to use these python codes to retrieve a .fasta file from gene database, but the output were the parameters of the report
...
- 15
3
votes
2
answers
282
views
How to obtain NCBI Nucleotide (Entrez) IDs for all E coli sequences?
I would like to gather a list of ALL E coli NCBI (Entrez/Nucleotide) IDs so that I can download fna and faa files, through a function like this:
...
- 33
1
vote
0
answers
32
views
Finding annotated counterpart after BLASTn with efetch (Biopython)
I am creating a pipeline for the identification of unknown transcripts. After a local BLASTn search of the transcripts, I have a large list of the respective hits with different genomes. I have the ...
- 26
2
votes
1
answer
52
views
Why doesn't an (Entrez eutils) einfo request for "gene" return the link gene_nucleotide or gene_nucleotide_pos links?
I'm updating a galaxy tool wrapper for Entrez's eutils suite and I'm trying to create a form with valid link selections (among other things) based on the "from" & "to" ...
- 221
0
votes
1
answer
51
views
How to extract metadata from NCBI's experiment?
I want to extract metadata from experiment SRX1596422. I have sratoolkit and Entrex direct but not sure what line of code to use. Here's the link for the experiment: experiment SRX1596422
3
votes
1
answer
145
views
How to query NCBI (Nucleotide database) by a feature qualifier?
I cannot seem to find a way to query nucleotide database (https://www.ncbi.nlm.nih.gov/nuccore) by a specific qualifier of the feature. For example, by /host under the feature "source".
For example, ...
- 33
1
vote
2
answers
112
views
Why the gene symbol aliases have significantly different sequences?
"Aliases" or "Synonyms" should represent the same gene but with different names. But when I try to find the sequence of one alias and try to match with another alias they are ...
- 35
1
vote
1
answer
69
views
rentrez to retrieve NIH files
I'm trying to use rentrez package to retrieve NIH files, and ran the following code (I followed what was on the rentrez tutorial):
...
- 11
4
votes
2
answers
435
views
Entrez.efetch returns incomplete genbank records
I am using the biopython Entrez.efetch command to retrieve all features (CDS, mRNA, ...) of some genomes.
In this case (NC_014649, Acanthamoeba polyphaga mimivirus), it works as expected:
...
- 595