Questions tagged [data-download]
The process of downloading data from the internet.
49
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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 ...
- 605
0
votes
1
answer
42
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How to download multiple UniRef clusters with all their members?
We are trying to download multiple UniRef clusters in one batch on the website. However, it seems the members are not downloaded... Could you guide me a way to the solution? Many thanks!
For example, ...
CommunityBot
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1
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How can extract the list of genes name from the raw data in GEO?
The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R?
I would ...
CommunityBot
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0
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44
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ZINC15 database: proxy server error when trying to download catalog in any format
I am a complete beginner in the use of such databases.
When navigating to the ZINC15 database website and trying to download an entire catalog with the "Download all as" option the request ...
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9
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Where would I get the activity profile dataset for Lantus Solostar insulin, and for other diabetes treatments such as Metformin?
I am working on a personal project for a better, more informed management of my own Diabetes Mellitus, Type 2 (aka "T2DM", or "T2D"). With some difficulty I am able to access and ...
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1
answer
39
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Where can you download functional domain labels of the human genome?
I'm visualizing where mutations occur in a gene, and would like to add functional domains to the plots.
I have some trouble locating sources to download data on functional domains.
The dataset should ...
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0
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28
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Exporting Panther functional classification of gene list
After inputting a list of gene and running an analysis in https://www.pantherdb.org/ (such as "functional classification"), I get a result table that is limited by an X number of entries ...
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2
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130
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Where to download a file with major and minor alleles at every position?
I want a list of all variants, i.e. sites which are known to vary between human to human. For example, it should ideally cover all sites in here, but without samples.
I don't want a giant reference ...
17
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6
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5k
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What's the best way to download data from the SRA? Is it really this slow?
I'm trying to download three WGS datasets from the SRA that are each between 60 and 100GB in size. So far I've tried:
Fetching the .sra files directly from NCBI's ftp site
Fetching the .sra files ...
- 193
3
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2
answers
5k
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How to download the whole BLAST nt database into a specific folder?
I have successfully downloaded the whole nt BLAST database into the current folder using:
wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz"
However, I ...
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41
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Get BioProject code of a GEO dataset
In publications the GEO code is usually shared and not the BioProject/study code.
I want to get the BioProject/Study Accession code of a GEO dataset (to later download the data from ENA).
I know that ...
- 14.9k
4
votes
1
answer
116
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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 ...
- 613
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4
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1k
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How to download ligands for PDB structure
I have some PDB IDs and for every structure, I need all its ligands, so I want to automate the process.
The ligands are different for every chain:
...
- 2,464
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109
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Problem with nextflow -resume and path.fromSRA
I have a problem with nextflow -resume
Here is my script :
...
- 41
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0
answers
50
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Download Addgene database
Is anyone aware of a way to download all vector sequences from addgene at once? As a non-profit, I'd assume they shouldn't be opposed to making this data available, but it doesn't seem to be possible. ...
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2
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2k
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3
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1
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Downloading genes from NCBI in fasta format
I'm pretty new in bioinformatics.
I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download ...
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2
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1k
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How to wget a gff from NCBI database?
Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this is here.
However, I do not see ...
4
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0
answers
44
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Retrieve protein sequence from Mgnify given only accession code
I only have the accession codes of several proteins from the MGnify database (https://www.ebi.ac.uk/metagenomics/). I would like to retrieve the full amino acid sequence data from the database, but I ...
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1
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How to get coding sequences (CDS) of UniProt reference proteomes?
I downloaded the following reference proteomes:
https://ftp.ebi.ac.uk/pub/databases/reference_proteomes/QfO/
...
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1
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How do I download the mitochondrial haplogroup datasets for human genetics online?
I seem to have landed on the mitomap.org site, but I don't know what to make of it or what do with it / how to get the genomes onto my computer. It sounds like the genomes are stored in GenBank, but ...
CommunityBot
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1
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2k
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Download or create VCF from Human Genome Diversity Project (HGDP)
I can't seem to find HGDP data in VCF format.
Does anyone know where I can download it from?
Perhaps there a Snakemake pipeline for calling VCFs from this data?
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2
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1
answer
108
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Taking too long to download metadata file (estimated size 30MB) from Covid-19 Data Portal
I am working on developing a tool to classify covid variants. So I am trying to download SARS-CoV-2 sequence data along with lineage annotation from Covid-19 Data Portal (I could not find a better ...
M__♦
- 12.8k
2
votes
2
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341
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Replacing column 1 in file1 with matching ID's in file 2
I have downloaded two files:
File1.csv from:
https://depmap.org/portal/download/data_slicer/download?file_path=20220227%2F3c335b7d-c18e-4788-b2e6-512d71f0a339%2Fexport.csv&name=Metabolomics.csv
...
- 395
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2
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683
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What happened to sra ftp server?
My whole (professional) life I am downloading sequences from SRA and ENA databases. Long time ago, I used prefetch from sra-tools, but later I switched to simply using wget from ftp servers of the two ...
- 14.9k
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2
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47
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Understanding exercise on file coverage with question on summary statistics
I'm doing an exercise that asks for two files:
Input 1: A target file (.bed format) contains multiple regions from
...
- 10.5k
1
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1
answer
380
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Where to find publicly available Sanger chromatography data?
I am looking for any public available databases where I can download Sanger chromatography data ideally in Ab1 or SCF file format. I need extremely large amounts of this, since I want to use it for ...
- 151
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1
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How to download data from SRA in Linux systems via the command line?
My workflow for downloading data from SRA has been the following:
Access SRA Run Selector.
Enter the accession number for the project of interest.
Download "Accession List" for the "...
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7
answers
16k
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Download multiple SRA files
I want to download all SRA file from the following project. Is there a method to download all the SRA files at the same time?
5
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4
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280
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How do you query and explore ENCODE data?
I am looking for a modular way to query data from ENCODE.
For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it?
Finally, is there an ...
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3
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5k
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Download multiple fastq files using fastq-dump
I want to download the following fastq files at the same time in Salmon:
- SRR10611214
- SRR10611215
- SRR10611215
- SRR10611216
- SRR10611217
Is there a way ...
- 221
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0
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207
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Trying to download a large number of files from ENA programmatically
I am downloading a large number of files from the ENA in Python using Multithreading. As an example, to be more concrete, I tried downloading 12 files simultaneously using 12 threads. I noticed that ...
4
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2
answers
859
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Downloading all COI sequences from BOLD fails
I have metabarcoding sequence data (COI) from bulk animal samples (including arthropoda, nematoda, annelida, mollusca) and I want to BLAST all of these sequences. I used following command to do this: <...
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39
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Blood analysis devices: how and where is the data saved
I've read that there are blood analysis devices that can automatically determine the data for each specified analyse. You can expect to get the results in less than a day.
Q: How and where do they ...
2
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2
answers
356
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How to download multiple proteomes at once?
I'm looking for a way to download multiple proteomes at once from one clade, as fasta. Probably from the NCBI, because it looks more user-friendly than Ensembl, but Ensembl is okay too. In the best ...
- 1,286
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2
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246
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GDC data portal cancer subtype
I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (https://portal.gdc.cancer.gov/repository) to classify breast cancer subtypes (luminal ...
- 156
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votes
2
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270
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How to link GDC ids to CCLE cell line names?
Hello bioinformaticians,
I've recently downloaded few RNAseq data files from Genomic Data Commons Data (GDC) portal. These files belong to Broad institutes CCLE project.
Now the problem is that GDC ...
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1
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How to query the Human Microbiome Project (HMP) to find all subjects with both 16s and WGS workups?
I am looking for a query to run on the HMP database that will return all subjects who have had BOTH 16s and whole genomes sequence (WGS) workups. I am currently using this query...
...
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4
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2k
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Convert SRA to FastA
I'm trying to get the FastA files for some accessions (like NC_001416.1). I did not managed to find an FTP server or direct link to these files (I want to get it from command line with ...
- 3,958
6
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1
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647
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Download data from the Human Microbiome Project via ascp
I have asked this question in biostars, but I am trying here as well as people working with "omics" data might be able to help. I think my issue relates understanding how large data storage on online ...
CommunityBot
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Where can I find the DNA sequence of the C. elegans rRNA cluster?
Where can I find the DNA sequence of the C. elegans rRNA cluster?
Ideally, I would be able to do it using the command-line.
I've tried using NCBI but the results are unsatisfactory. I am interested ...
- 2,479
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1
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477
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How to download SNP data from specific regions, population and positions?
I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems.
To do that, I've read a lot of papers and books in order to understand the main ...
CommunityBot
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5
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2
answers
736
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A reliable fetcher of short read using SRA/ENA accession
I am trying to build a workflow that gets data automatically from databases of sequencing reads (SRA - sequence read archive, ENA - european nucleotide archive). Till now I was pulling everything from ...
- 5,632
6
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1
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499
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How to validate that BAMs have been downloaded correctly?
I currently have several hundred BAM files which were downloaded by someone else. These have remained untouched---before working with them, I would like to double-check that these BAMs have been fully ...
CommunityBot
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2
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1
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154
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SNP data Download Help
I am new to the field of Bioinformatics. Single Nucleotide Polymorphism or SNP data are available on the the Internet to download.SNP related data are valuable for variety of reasons ranging from ...
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1
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288
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How to download gene expression data from NCBI gene database
In the NCBI gene database, I can add the expression tracks (circled in picture blow) through 'Tracks' button, but How I can download the expression data directly, not just look the picture?
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1
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998
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How to download the whole directory of an ensembl FTP page?
I am interested in downloading all the files at:
ftp://ftp.ensembl.org/pub/release-91/embl/bos_taurus/
I know how to download a single file from that page using wget (Unix) or download.file() (R) ...
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How to dump genes from GenBank in GFF3 format?
This question has also been asked on BioStars
If I look at this record in GenBank I see about 6k genes:
https://www.ncbi.nlm.nih.gov/nuccore/CM000760?report=gbwithparts
I'd really like to be able to ...
- 14.9k
6
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1
answer
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Stable download URLs
One big problem that I'm regularly facing is that URLs for downloading Bioinformatics data (e.g., RefSeq releases or NCBI genome releases) disappear.
Does anyone have any good solution for this?
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