Questions tagged [entrez]
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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68
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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. ...
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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:
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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 ...
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291
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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:
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53
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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 ...
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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
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227
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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:
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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 ...
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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" ...
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49
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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
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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, ...
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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 ...
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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):
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390
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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:
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