Questions tagged [ncbi]
The ncbi tag has no usage guidance.
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getting NCBI TAXname by R
I have a data frame on R, called qIns8, with 14 columns and 204 rows. the column called "subject tax id" has NCBI taxIDs for the corresponding row, I need a script to add another column to ...
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2
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How can I limit blast results to exclude a specific taxonomic ID?
I would like to perform blast+, using the command line, here is the code:
-task blastn -db nr -outfmt 7 -query myQuery.fas -out result.txt -remote.
I have to ...
-1
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37
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error in downloading the annotation of sequences on NCBI
I have developed an R function to download the "organism" name of the numerous NCBI accession numbers which are already saved in an object.
The function:
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71
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How to BLAST a protein against a large set of organisms?
I have a list of organisms with their full scientific names and Taxonomy IDs, total ~1500. I want to BLAST my protein against this 1500 genome or proteome. How can I do that?
Here a sample protein ...
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Shell script to validate fastq issue
I have two GSM ID as test case where both of them are having data when I checked through sra explorer tool but when I try to fetch through a script only one of them returns output where the other one ...
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Linking GenBank records to biosamples (and vice versa) using edirect
Assume that I wish to find all complete human mitochondrial genome records on GenBank (or rather, NCBI nuccore) that also have an entry in NCBI's Biosample database.
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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 ...
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183
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ncbi fastq dump error in loop
I have a very basic objective which I want to give list of id to a ncbi-srafastq tool kit which will prefetch the id which is in .sra file extension and then it will run fastq-dump on the file to ...
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73
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Reference genome (bwa -mem)
I want to do mapping with bwa mem. I downloaded a reference genome from ncbi database which is (Danaus plexippus). I got one ncbi_database.zip file which contain 2 ...
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Different human reference genomes from NCBI and ENSEMBL, and variant annotation with Variant Effect Predictor (VEP)
Background: I have been working on a human variant calling pipeline, from whole exome reads to variant annotation.
For variant annotation I used the Variant Effect predictor (VEP), which is Ensembl ...
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23
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adding multiple files in folder and zipping in loop
Through fasterq-dump, I am generating 2 files in 1 run of loop. I want to club these two files (A_1.fastq & A_2.fastq) in one folder and zip the it.
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189
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ZIP the fasterq-dump files in loop
I want to zip the files generated by fasterq-dump simultaneously as they are generated. The code that I tried is this.
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28
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How important are the homozygous variants that get unnecessarily deleted using liftover?
I'm referring to the text described here:
These tools [NCBI remap, CrossMap] operate only on the sites present in an input VCF, and return the representation of those sites in a new genome assembly. ...
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81
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Prokka + table2asn (NCBI submission)
I have a couple of MAGs of interest that I am trying to submit to the NCBI (with annotations).
The process of submitting the annotations is rather challenging to me. I have the output of Prokka, which ...
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NCBI Blast databases - cannot find some databases
I'm working with a system that does local BLAST searches using some preconfigured BLAST databases. From what I see, these were updated within the last year, but I cannot find any current databases ...
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80
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How to get the nucleotide sequence for protein NCBI accession code, programatically?
It is a lot easier in my work to do blast searches against protein databases when I can, since I work with distantly related organisms. But sometimes, I need to work with the actual nucleotide ...
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How do you go about grabbing proper genotyping infomation from dbSNP using entrez API?
I made an R function to grab rsID genotypes from dbSNP using the entrez API. For example, here is the xml output that I am trying to parse:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=...
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How to access specific SRA sequences within an SRP file?
How do you get a specific 100 SRA sequences from a Bioproject which contains 400 runs, when you don't need all of them?
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145
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How do i search by these gene properties in NCBI's GenBank?
I want to search GenBank entries by gene product and taxon id.
Taking the 16s rRNA as an example for a gene and Piscirickettsia salmonis (taxon:1238) for a taxon:
https://www.ncbi.nlm.nih.gov/nuccore/...
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44
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Custom-made kraken2 catalogue
I am looking for instructions on creating a custom-made kraken2 catalogue from the sequences of my choice and the corresponding phylogenetic tree in newick notation.
I will appreciate an input on ...
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What is the NCBI's definition of an "atypical genome"?
Using the new NCBI Datasets platform, you can browse the collection of genomes associated with one or more taxa. For example, searching Pseudomonas aeruginosa returns 19,878 genomes as of 29 March ...
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Kraken2 Standard Database failing to build (unexpected FTP path)
I am attempting to build just the standard Kraken2 Database by using the following command:
kraken2-build --standard --threads 24 --db $DBNAME
I am returned the ...
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1
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77
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how to do manual search on NCBI with biopython and add link to publication
I'm trying to reproduce a complex manual search on NCBI using BioPython, but obviously something is not right. My command line is not working, but I'd especially like a way to have an accurate search ...
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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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