Download sra fastq files

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. 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.

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! Improve this question.

Add a comment. Active Oldest Votes. Improve this answer. Kai Fung Kai Fung 11 1 1 bronze badge. Geo Vogler Geo Vogler 3 1 1 bronze badge. The text file can be any list of accessions, separated by return. Tested in Bash. If there are potential problems with the Sample ID, context-sensitive warnings are shown below the table in the left corner of the window. Downloading FASTQs and metadata with default settings would result in assembling multiple SRA runs of the same SRA experiment together once a pipeline with default file naming parameters would be started.

Similar, if there would be SRA samples with the same Strain Name also those reads would assemble wrongly together. For versions under 2. Alas with the new version, you would need to run them like so:. Just remember that commands and examples in training materials may not work correctly anymore. Some people claim that prefetch can download fastq files with. Subsequent conversions with fastq-dump will take 1 minute since it uses the cache file. The download was slow, estimated time of 15 minutes, I did not wait to finish.

The next day I tried again the download seemed much faster under a minute. Your mileage may vary. Be sure to use the —split-3 option, which splits mate-pair reads into separate files. For paired-end data, the file names will be suffixed 1. FASTQ and 2. FASTQ; otherwise, a single file with extension.