Download fastq files public

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 After you have downloaded the SRA file, you can use the command fastq-dump to extract the contents of it into a.

A sample command to extract SRR We observe that two fastq files have been extracted from SRR This is because the original data was produced from paired-end sequencing, which usually has both a Read1 file and Read2 file. I typically use the settings provided above for fastq-dump as my default settings. Since there are lots of SRA files associated with our samples, it would take a long time to manually run prefetch and fastq-dump for all the files.

To automate this process, I wrote a small script in python to first download each SRA file using prefetch and then run fastq-dump. After running the python script, our FASTQ files should all be sitting in a directory called 'fastq'. I would advise against it, since I have found this method to be much slower than first running prefetch and then fastq-dump on the pre-downloaded SRA files. Here's some proof, in which I time the processes below:. In comparison, running fastq-dump without pre-downloading the files for the same SRA ID took a total time of 77 minutes 34 seconds!

Now, we can start mapping the reads to a reference genome and perform downstream bulk RNA-sequencing analysis. I hope that this short tutorial has helped you learn how to use the SRA tools to download raw sequencing data. Thanks for reading! Skip to content. Star 2. Branches Tags.

Mostly, we download sra files for the purpose of getting corresponding fastq or sam files, so as to use them in our own pipeline for downstream analysis. If not, go to SRA database. First Choice — Aspera Connect. It is a commercial high speed file transfer software produced by IBM. Many sites can transfer data at Mbps. Search PyPI Search. Latest version Released: Nov 14, No project description provided.

Navigation Project description Release history Download files. Statistics View statistics for this project via Libraries. Maintainers tpob. Project details Statistics View statistics for this project via Libraries. Download files Download the file for your platform. Files for fastq-downloader, version 0.