Questions tagged [entrez]

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2 votes
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Different ClinVar classifications/SNPs are linked to the same rsid

I am using R to extract ClinVar classification of SNPs using rsid. Here's an example of my workflow: Patient data: Sample Func Gene Codon_Change dbSNPv151_GRCh38 Chr Start End Ref Obs Mary ...
benson23's user avatar
  • 171
2 votes
1 answer
57 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: ...
The August's user avatar
2 votes
0 answers
79 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 ...
Freek's user avatar
  • 563
1 vote
1 answer
143 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: ...
Sudoh's user avatar
  • 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 ...
Sudoh's user avatar
  • 217
1 vote
2 answers
165 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 ...
Laura's user avatar
  • 909
2 votes
2 answers
528 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 ...
Sawason's user avatar
  • 21
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 ...
Glubbdrubb's user avatar
1 vote
2 answers
76 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. ...
weddegege's user avatar
0 votes
1 answer
13k 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: ...
Mario Cat's user avatar
1 vote
1 answer
1k views

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 ...
user345394's user avatar
2 votes
1 answer
533 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: ...
blammo69's user avatar
1 vote
2 answers
57 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 ...
user66081's user avatar
  • 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 ...
DurianDan's user avatar
3 votes
2 answers
300 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: ...
S.Chauhan's user avatar
3 votes
2 answers
49 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 ...
MWP's user avatar
  • 46
2 votes
1 answer
56 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" ...
hepcat72's user avatar
  • 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
Ophelia Vallee's user avatar
3 votes
1 answer
150 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, ...
hlex's user avatar
  • 33
1 vote
2 answers
121 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 ...
Riq's user avatar
  • 35
1 vote
1 answer
70 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): ...
lostindata's user avatar
4 votes
2 answers
451 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: ...
cmdoret's user avatar
  • 595