Questions tagged [ncbi]

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Liftover variants/vcf called on NCBI reference genome

I have been tackling this problem for a while now, and I hope someone has a better answer. I need to liftover variants (.vcf) from NCBI hg37 to NCBI hg38. The NCBI remapping tool has been depreciated. ...
Dandelion's user avatar
  • 313
2 votes
1 answer
73 views

How can I download multiple SRR* files at a time when using sratoolkit's fastq-dump?

I have multiple SRR files to download, and their accession is in a list: SRR9004325 SRR9004326 SRR9004327 I read the NCBI document but don't find how to achieve ...
Bioinfotec's user avatar
2 votes
1 answer
42 views

arm64 installation of AMRFinderPlus

I was trying to install NCBI AMRFinderPLUS on my Nvidia Jetson using standard Bioconda based installtion. However, all the time it is giving error that the package is not available and I thought I am ...
prekij's user avatar
  • 33
1 vote
1 answer
28 views

What does this BLASTN mean: Error pre-fetching sequence data?

I am trying to run BLASTN on a 14GB Pseudomonas database using the command: blastn -db ~/pseudomonas-db/pseudomonas -query ~/desktop/inputfiles/poz176.fasta -out poz176-out -num_threads 8 I get the ...
blackthorne18's user avatar
0 votes
1 answer
29 views

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 ...
Farzad Beikpour's user avatar
1 vote
2 answers
118 views

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 ...
Farzad Beikpour's user avatar
-1 votes
1 answer
39 views

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: ...
Farzad Beikpour's user avatar
2 votes
2 answers
81 views

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 ...
Supertech's user avatar
  • 606
3 votes
1 answer
147 views

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 ...
kcm's user avatar
  • 1,804
4 votes
0 answers
47 views

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. ...
Michael Gruenstaeudl'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
3 votes
1 answer
354 views

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 ...
PesKchan's user avatar
  • 207
3 votes
2 answers
104 views

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 ...
Moon's user avatar
  • 103
3 votes
0 answers
73 views

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 ...
Dandelion's user avatar
  • 313
0 votes
0 answers
25 views

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. ...
Shradha Sharma's user avatar
2 votes
2 answers
333 views

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. ...
Shradha Sharma's user avatar
1 vote
1 answer
29 views

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. ...
BigMistake's user avatar
1 vote
0 answers
144 views

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 ...
Laura's user avatar
  • 909
2 votes
1 answer
36 views

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 ...
KirkD-CO's user avatar
  • 175
2 votes
2 answers
112 views

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 ...
Laura's user avatar
  • 909
2 votes
0 answers
22 views

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=...
Blaze9's user avatar
  • 31
0 votes
0 answers
31 views

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?
K_081's user avatar
  • 149
2 votes
2 answers
176 views

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/...
Freezing Soul's user avatar
2 votes
0 answers
53 views

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 ...
Roger V.'s user avatar
  • 381
4 votes
1 answer
98 views

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 ...
acvill's user avatar
  • 613
1 vote
1 answer
170 views

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 ...
InterestingQuestions61's user avatar
2 votes
1 answer
87 views

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 ...
Marine Bergot's user avatar
1 vote
1 answer
144 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