Questions tagged [data-download]

The process of downloading data from the internet.

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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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2 votes
1 answer
23 views

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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  • 151
2 votes
1 answer
32 views

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 ...
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2 votes
2 answers
204 views

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 ...
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  • 159
3 votes
2 answers
103 views

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 ...
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1 vote
2 answers
30 views

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 ...
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  • 111
1 vote
1 answer
50 views

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 ...
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  • 151
2 votes
1 answer
588 views

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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1 vote
1 answer
57 views

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 ...
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  • 133
0 votes
1 answer
971 views

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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1 vote
3 answers
2k views

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 ...
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1 vote
0 answers
164 views

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 ...
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3 votes
2 answers
469 views

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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2 votes
2 answers
169 views

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 ...
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0 answers
39 views

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 ...
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1 vote
1 answer
57 views

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 ...
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5 votes
4 answers
244 views

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 votes
2 answers
215 views

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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6 votes
4 answers
1k views

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 ...
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  • 221
3 votes
1 answer
70 views

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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0 votes
2 answers
203 views

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 ...
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1 vote
1 answer
26 views

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 ...
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1 vote
1 answer
339 views

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 ...
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5 votes
2 answers
612 views

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 ...
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6 votes
1 answer
231 views

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 ...
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  • 1,363
2 votes
1 answer
140 views

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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3 votes
1 answer
210 views

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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2 votes
1 answer
594 views

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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2 votes
1 answer
4k views

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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2 votes
2 answers
1k views

Downloading URL using AWK for fixed fields

I have a text file as follows ...
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6 votes
1 answer
500 views

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 ...
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6 votes
7 answers
10k views

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?
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4 votes
2 answers
516 views

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 ...
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17 votes
5 answers
3k views

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 ...
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  • 171
6 votes
1 answer
101 views

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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