How long should it take to download fastq files

This is the most widely used format in sequence analysis as well as what is generally delivered from a sequencer. Many analysis tools require this format because it contains much more information than FastA. The format is similar to fasta though there are differences.

It can take some time to download the file since it's very big. Firefox will give you an estimate on how long it's going to take. A PDF of this tutorial is available for download.

Basic Statistics. Let's say you are reading a paper in a journal and see an interesting RNA-seq experiment. You decide that you want to sift through the data for your own genes of interest. The first step is finding the GEO accession number corresponding to the dataset. If that doesn't work, try to search for "GEO". Once we have the accession number, we can now search GEO to find the dataset. The purpose of this analysis was to explore the genes that splenic dendritic cells upregulated upon stimulation.

Following the link, we can see all the details associated with the study. If we scroll to the bottom of the page, we should see a list of samples as well as a link to the SRA Run Selector , which I've pointed out in the following image:. I've pointed out where to find them in the image below:. The SRA runs e. SRR correspond to the actual sequencing files that we want to download in order to access the raw data.

This means that the lab had deposited multiple FASTQ files for one sample and did not bother to concatenate them together prior to deposition.

You can get more details about how each sample was prepared clicking on the GSM identifier in the Samples section from the first image e. This will take you to the sample description page. Although it's more work, I prefer clicking through these pages for each individual sample because they provide important information such as how the libraries were prepared. I have summarized the different identifiers for GSE in the following table:.

But what is a. If you are using a Linux platform, you can type: apt install sra-toolkit in your command line to install the toolkit. The file SRR Downloading SRA fastq files through ftp over long distance could take long time and should consider using using 'fasp'. Author s Jack Zhu. It can take some time to download the file since it's very big.

Firefox will give you an estimate on how long it's going to take. FASTQ files can contain up to millions of entries and can be several megabytes or gigabytes in size, which often makes them too large to open in a normal text editor.