SRA Toolkit DocumentationBack to List of the Tools
sff-dump [options] <path/file> [<path/file> ...]
sff-dump [options] <accession>
Frequently Used Options:
|-h|||||--help||Displays ALL options, general usage, and version information.|
|-V|||||--version||Display the version of the program.|
|-N|||||--minSpotId <rowid>||Minimum spot id.|
|-X|||||--maxSpotId <rowid>||Maximum spot id.|
|-G|||||--spot-group||Split into files by spot group ("read group").|
|--spot-groups <[list]>||Filter by spot group (read group): name[,...].|
|-R|||||--read-filter <[filter]>||Split into files by value. Values:pass|reject|criteria|redacted.|
|Workflow and piping:|
|-O|||||--outdir <path>||Output directory, default is working directory ('.').|
|-Z|||||--stdout||Output to stdout, all split data become joined into single stream. Note that this is the BINARY output, does not stream sff.txt. Useful for piping to another program.|
|-T|||||--group-in-dirs||Split into subdirectories instead of files.|
|-K|||||--keep-empty-files||Do not delete empty files.|
Produces a small sff file from the first 100 reads (-X 100). This is useful for verifying the formatting options before dumping a whole data file.
sff-dump -X 100 SRR996643
Allows you to view the data in sff.txt (human readable) format. With the 454 utility 'sffinfo' installed, this command dumps sff to stdout (-Z), pipes it to sffinfo ("-" needed for sffinfo to accept from stdin), and then to 'less' for viewing.
sff-dump -Z SRR996643 | sffinfo - | less
Possible errors and their solution:
This error indicates that the .sra file cannot be found. Confirm that the path to the file is correct.
item not found while constructing within virtual database module - the path '<path>/SRR*.sra' cannot be opened as database or table
The data were not submitted as sff, thus we lack the information required to convert to sff. It is recommended that you dump into another format (fastq, sam, etc.).
This run cannot be transformed into SFF format. Conversion cannot be completed because the source lacks one or more of the data series required by the SFF format. You should be able to dump it as FASTQ by running fastq-dump.
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