org.nmdp.ngs.sra.xsd.SRA.run.xsd Maven / Gradle / Ivy
A run contains a group of reads generated for a particular experiment.
Short text that can be used to define submissions in searches or in displays.
The EXPERIMENT_REF identifies the parent experiment.
Experiment describes nucleic acid prepararation from biological sample,
molecular strategies and selections used in preparation of libraries for
sequencing.
The type of the run.
Data files associated with the run.
The READ_LABEL can associate a certain file to a certain read_label defined in the SPOT_DESCRIPTOR.
The name or relative pathname of a run data file.
The run data file model.
Sequence Read Archives native format in serialized (single file) form.
Standard Short Read Format file (.srf), all platforms
454 Standard Flowgram Format file (.sff)
Combined nucleotide/qualities sequence file in .fastq form.
Please see SRA File Formats Guide for definitions of the definition and restrictions on this form.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Tab delimited text file used to deliver certain auxiliary data along with sequencing submissions (only needed for certain
use cases). The first line is devoted to column headers. Each column is dedicated to an INDSC
data series type.
Please see SRA File Formats Guide for definitions of the definition and restrictions on this form.
A combination of 454 primary analysis output files, including
seq
qual
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
454 base calls (for example .seq or .fna).
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
454 quality scores (for example .qual).
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
A kind of fastq format specific to the Helicos platform.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
A combination of SOLiD primary analysis output files, including:
csfasta
_QV.qual
_intensity.ScaledCY3.fasta
_intensity.ScaledCY5.fasta
_intensity.ScaledFTC.fasta
_intensity.ScaledTXR.fasta
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Colorspace calls (for example .csfasta)
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Colorspace quality scores (for example .qual)
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Pacific Biosciences Hierarchical Data Format. Please see
SRA File Formats Guide for definitions of these file formats.
Binary SAM format that combines alignment and sequencing data.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Binary CRAM format that combines alignment and sequencing data.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
Please see SRA File Formats Guide for definitions of these file formats,
and the SRA Submission Guidelines document for data series that are appropriate for your study.
Sequence and qualities are minimally required.
How the input data are scored for quality.
The quality score is expressed as a probability of error in log form:
-10 log(1/p) where p is the probability of error, with value range 0..63,
0 meaning no base call.
The quality score is expressed as the ratio of error to non-error in log form:
-10 log(p/(1-p)) where p is the probability of error, with value range -40..40.
The SRA will convert these into phred scale during loadtime.
Character used in representing the minimum quality value.
Helps specify how to decode text rendering of quality data.
ASCII character based encoding.
Single decimal value per quality score.
Single hexadecimal value per quality score.
Character used in representing the minimum quality value. Helps specify how to decode text rendering of quality data.
ASCII value 33. Typically used for range 0..63.
ASCII value 64. Typically used for range 0..60.
Checksum method used.
Checksum generated by the MD5 method (md5sum in unix).
Checksum of uncompressed file.
Checksum of unenrypted file(used in conjunction with checksum of encrypted file).
Allow for an individual DATA_BLOCK to be associated with a member of a sample pool.
Links to resources related to this RUN or RUN set (publication, datasets, online databases).
Properties and attributes of a RUN. These can be entered as free-form
tag-value pairs. For certain studies, submitters may be asked to follow a
community established ontology when describing the work.
ISO date when the run took place.
If applicable, the name of the contract sequencing center that executed the run.
Example: 454MSC.
RUN_SET serves as a container for a set of runs and a name space
for establishing referential integrity between them.