10
votes
How to extract metadata from NCBI's short read archive (SRA) for a few runs?
Entrez Direct is perfect for this sort of thing. You can do something like this:
...
- 1,126
10
votes
Accepted
Importing GFF file with Biopython
No, there is currently no GFF support in biopython.
However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like <...
- 3,061
9
votes
Accepted
How to download FASTA sequences from NCBI using the terminal?
Alternatively, you can use the NCBI Entrez Direct UNIX E-utilities
Basically, you have to download the install file here: https://www.ncbi.nlm.nih.gov/books/NBK179288/bin/install-edirect.sh
In the ...
- 1,021
7
votes
Accepted
Why do these NCBI representative genomes for ape species have no Y chromosome?
tl;dr: technical difficulties, or sex
For the gorilla, that genome is from a female gorilla (Kamilah the gorilla) so she doesn't have a Y chromosome.
For the chimp link, there is a visualization of ...
- 2,547
6
votes
How do you download stuff from NCBI fast?
Answers to this question can be found on biostars. To give you a short summary:
Faster way might be to use the parallel-fastq-dump, as suggested in this answer. I ...
- 3,521
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
How do I pull singe cell RNA sequencing data from GEO database?
The simplest would be using a count matrix (at the end of the link you have shared, section "Supplementary file"). For example ...
- 3,472
5
votes
How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?
I would just blast it. When blasting locally, you need to first make a database from your genome, so assuming you got the command-line version of blast installed you can do something like
...
- 5,287
5
votes
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How to get the number of complete phage genomes available on ncbi?
Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore
Copy and paste the search term:
...
- 6,992
4
votes
How to export web NCBI tBLASTn results in table format with many queries?
It sounds like your easiest option is to just install blast on your local machine and set up the databases there. It really will only take a few minutes to blast 6,000 sentences against a yeast genome ...
- 3,061
4
votes
4
votes
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CDS length for each human gene
While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for ...
- 7,957
4
votes
Accepted
How to retrieve the DNA sequence from a particular species and region through command line?
Samtools
Samtools is a toolkit that includes a binary called samtoools, which can be used to query a FASTA file — to extract a subsequence based on some coordinate ...
- 3,045
4
votes
How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?
In your sequence header you will see:
[location=complement(940023..940580)]
It's a reverse strand gene. Reverse complement the sequence, then search the genome ...
- 1,699
4
votes
Is there a publication database or search engine offering geneID or UniProtID correlation?
I think this could be close to what you're looking for: http://glad4u.zhang-lab.org/index.php
Paper: GLAD4U: deriving and prioritizing gene lists from PubMed literature
It works with gene names though,...
- 1,378
3
votes
Accepted
NCBI retrieve genome assembly with splicing or "modifications"
The page you link to is a GenBank Flat file, the default format used by GenBank. So, to get that format, which includes the join lines, use:
...
- 7,957
3
votes
Accepted
ncbi...eutils/esearch.fcgi: How to search now in the snp database?
eUtilities for dbSNP is in the process of being retired. See this post from NCBI. You may want to check out the new API.
From the NCBI Insights blog post:
Entrez search is available only for human. ...
- 1,126
3
votes
Genomics: Downloading genomic data from the NCBI Genbank database
For downloading data from commandline use the E-utilities of NCBI.
- 273
3
votes
Download proteomes from NCBI based only on binomial names
The general procedure is explained here:
First step is to search the Taxonomy database with the organism name. Accepted common names usually work at all taxonomic levels. Use the scientific name or ...
- 451
3
votes
Accepted
How to automate NCBI genome download
Outline of solution:
get this file: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt
filter for lines having "Complete Genome" in column 12
filter for lines having a taxid (...
- 423
3
votes
NCBI xml-format Printing nodeValues from tags with the same names
use a XSLT processor (http://php.net/manual/en/class.xsltprocessor.php) with the following stylesheet.
...
- 1,473
3
votes
NCBI SRA database sample: control vs test
You can download the information using this link:
I did it in R:
...
- 1,638
3
votes
BWA: Detecting Variation between Reference Genome and Short-Read Sequences
I haven't done any whole-genome STR analysis from NGS data myself, but are aware of others that have used lobSTR for this. There's also a recent paper [here] that compares a few different STR analysis ...
- 11.5k
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 ...
- 19.3k
3
votes
Accepted
Programmatically retrieve Metadata from SRA Run Selector
Depending on exactly which information you seek, you can try:
esearch -db sra -query 'PRJNA491191[bioproject]' | efetch -format native -mode xml
This will return ...
- 1,126
3
votes
Accepted
What does this accession NCBI code mean: 6MWN_B?
In general, an accession is a value that points to (provides access to) a single database entry. Different databases (GenBank, RefSeq, Ensembl, SwissProt, and so on) have different conventions for ...
- 4,898
2
votes
How to automate NCBI genome download
As an alternative, you can use the NCBI Datasets CLI, in a two step process to generate a dehydrated dataset for later hydration:
...
- 66
2
votes
Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number
You can use Entrez Direct for this as follows:
efetch -db protein -id YP_805528.1 -format gpc -mode xml | xtract -insd Protein EC_number
YP_805528.1 6.3.2.13
- 1,126
2
votes
How to extract metadata from NCBI's short read archive (SRA) for a few runs?
Here's a very crude script version, which should work without downloading fancy software tools. It will only work as long as the website stays in its current layout.
It extracts the particular ...
- 309
2
votes
Importing GFF file with Biopython
I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.
The only downside is that I believe it is no longer ...
- 334
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