The hisat program can automatically download SRA data as needed. In some cases, users may want to download SRA data and retain a copy. To download using NCBI's 'prefetch' tool, you would need to set up your own configuration file for the NCBI SRA toolkit. Use the command vdb-config to set up a directory for downloading. This will download the SRA file (in sra format) and then convert them to fastq file for you. If your SRA file is paired. In cases were you cannot run the SRA toolkit or any other programs to download the file, you can still use the inbuilt commands of Linux such as wget and curl. The standard web link for downloading the SRA. Now we will see the commands for uninstalling the sra-toolkit from Ubuntu 16.04. For uninstalling this package you can easily use the apt command and remove the package from Linux Operating System. To remove the sra-toolkit following command is used: sudo apt-get remove sra-toolkit. Following command is used to remove the sra-toolkit package.
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