Fetch Data


fastq-dump [options] <accession>


-h | --help Displays ALL options, general usage, and version information.
-V | --version Display the version of the program.
Data formatting:
--split-files Dump each read into separate file. Files will receive suffix corresponding to read number.
--split-spot Split spots into individual reads.
--fasta <[line width]> FASTA only, no qualities. Optional line wrap width (set to zero for no wrapping).
-I | --readids Append read id after spot id as '' on defline.
-F | --origfmt Defline contains only original sequence name.
-C | --dumpcs <[cskey]> Formats sequence using color space (default for SOLiD). "cskey" may be specified for translation.
-B | --dumpbase Formats sequence using base space (default for other than SOLiD).
-Q | --offset Offset to use for ASCII quality scores. Default is 33 ("!").
-N | --minSpotId Minimum spot id to be dumped. Use with "X" to dump a range.
-X | --maxSpotId Maximum spot id to be dumped. Use with "N" to dump a range.
-M | --minReadLen Filter by sequence length >=
--skip-technical Dump only biological reads.
--aligned Dump only aligned sequences. Aligned datasets only; see sra-stat.
--unaligned Dump only unaligned sequences. Will dump all for unaligned datasets.
Workflow and piping:
-O | --outdir Output directory, default is current working directory ('.').
-Z | --stdout Output to stdout, all split data become joined into single stream.
--gzip Compress output using gzip.
--bzip2 Compress output using bzip2.

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