SRA Toolkit Documentation
Back to List of the ToolsTool: illumina-dump
Usage:
illumina-dump [options] <path/file> [<path/file> ...]
illumina-dump [options] <accession>
Frequently Used Options:
General: | ||||
-h | | | --help | Displays ALL options, general usage, and version information. | |
-V | | | --version | Display the version of the program. | |
Data formatting: | ||||
-A | | | --accession <accession> | Replaces accession derived from <accession> in filename(s) and deflines. | |
-x | | | --qseq <1|2> | Output QSEQ format: whole spot (1) or split by reads (2). | |
Filtering: | ||||
-N | | | --minSpotId <rowid> | Minimum spot id. | |
-X | | | --maxSpotId <rowid> | Maximum spot id. | |
-G | | | --spot-group | Split into files by spot group ("read group"). | |
Workflow and piping: | ||||
-O | | | --outdir <path> | Output directory, default is working directory ('.'). | |
-Z | | | --stdout | Output to stdout, all split data becomes joined into a single stream. | |
--gzip | Compress output using gzip. | |||
--bzip2 | Compress output using bzip2. |
Use examples:
Produces file with SRR# accession in filenames and deflines replaced with "sample1" (-A sample1)
in qseq format with non-split spots (--qseq 2).
Produces the sequence reads only (-r), writes the output to a sub-directory "Illumina" in the
CWD (-O Illumina) and gzips the file(s) (--gzip).
illumina-dump -A sample1 --qseq 2 SRR390728
illumina-dump -r -O Illumina --gzip SRR390728
Possible errors and their solution:
This error indicates a malformed command line, check your dump command for proper typos and proper usage of options.
This error indicates that the .sra file cannot be found. Confirm that the path to the file is correct.
param incorrect while reading argument list within application support module
item not found while constructing within virtual database module - the path 'SRR*' cannot be opened as database or table