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SRA Toolkit Documentation

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Tool: sra-stat

Usage:
sra-stat [options] <path/file> [<path/file> ...]
sra-stat [options] <accession>
Frequently Used Options:
General:
-h | --help Displays ALL options, general usage, and version information
-V | --version Display the version of the program
Output formatting:
-x | --xml output as XML, default is text
-s | --statistics calculate READ_LEN average and standard deviation
Filtering:
-a | --alignment <on | off> print alignment info, default is on
-b | --start <row-id> starting spot id, default is 1
-e | --stop <row-id> ending spot id, default is max
-q | --quick quick mode: get statistics from metadata; do not scan the table
--option-file <file> Read more options and parameters from the file.
Use examples:
sra-stat --quick --xml SRR390728
Outputs the stats for the data file in XML format (--xml) using existing metadata present in the file (--quick). Note that running sra-stat without "--quick" requires a scan of the entire file, and can be quite slow. Running sra-stat without "--xml" results in a minimal output.
sra-stat --xml --statistics SRR390728
Computes the read length statistics for the data set. Note that "--statistics" precludes "quick" mode and can be quite slow.
Possible errors and their solution:
directory not found while opening manager within virtual file system module
This error indicates that the .sra file cannot be found. Confirm that the path to the file is correct.
...failed with curl-error 'CURLE_COULDNT_RESOLVE_HOST'
The toolkit is attempting to contact or download data from NCBI, but is unable to connect. Please confirm that your computer or server has Internet connectivity.