Download and compress fastq files linux

You can contact me at surendra linuxnix dot com. Tar The purpose of the tar command, which stands for tape archive, is to merge multiple files into a single file. Post Views: 1, The following two tabs change content below. Bio Latest Posts. 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.

Rinzwind Rinzwind k 37 37 gold badges silver badges bronze badges. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name. Email Required, but never shown. The Overflow Blog. 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. Thank you Reply. Leave a Reply Cancel reply. Follow us in twitter Follow SixthResearcher.