Questions tagged [data-download]

The process of downloading data from the internet.

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ICD10 code list

I'm running some analysis on a large list of records with ICD10 codes. I'd like to join the data to the code description. I'm aware of where to find the exact codes, e.g. https://www.plasticsurgery....
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35 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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160 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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411 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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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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137 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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2answers
61 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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37 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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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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4answers
188 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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2answers
160 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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Where can I find hemagglutination inhibition (HI) assay data?

I am looking for hemagglutination inhibition assay data for type A influenza virus. Could someone please give me a link to a database with this information? Thanks.
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802 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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1answer
66 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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2answers
173 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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1answer
24 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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1answer
264 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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Viral Load and Antiretroviral Therapy Dataset

My project is on Mathematical Modeling of the relationship between viral load and antiretroviral therapy. Its purely an academic one which is exploratory in nature. Intend using the different ...
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2answers
449 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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1answer
177 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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1answer
132 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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1answer
166 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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1answer
373 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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1answer
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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2answers
916 views

Downloading URL using AWK for fixed fields

I have a text file as follows ...
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1answer
422 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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5answers
6k 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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429 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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5answers
2k 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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1answer
100 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?