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Data types

Name Presentation Description
AffyDirectory directory Affymetrix input directory for microarray CEL files.
AffyPGF file Affymetrix probe group file (PGF) that describes the microarray probe sets and the nucleotide sequences for them.
AgilentDirectory directory Agilent input directory.
AlignedReadSet file Base type for file formats that store aligned short reads.
BAM multifile Binary version of Sequence Alignment/Map format.
BAMHeader file Header for BAM file.
BAMIndex file Index for BAM files.
BAMList file A list of new-line separated bam files used as GATK multi-sample input.
BCF file Binary Call Format.
BED file Format for storing DNA region sets with optional scores for each region.
BinaryFile file Anything encapsulated into a single data file.
BinaryFolder directory Anything encapsulated into a single data folder.
Bowtie file Sequence Alignment/Map format for storing aligned short reads.
CSV file Rectangular CSV file with named columns.
Diff file Tab delimited file that lists the results of differential expression testing between samples for spliced transcripts, primary transcripts, genes, and coding sequences.
DNARegion file A list of genomic regions.
DNARegion2 file Set of DNA regions with annotations.
Eland file Aligned short reads from Illumina ELAND software.
FASTA multifile Sequence file.
FASTQ file Unaligned short reads with base pair quality information.
FASTQZ file Gzipped unaligned short reads with base pair quality information.
FCS file Flow Cytometry Data File Standard.
flowSet file Container for a set of flowFrame objects.
FPKM_tracking file FPKM tracking files use a generic format to output estimated expression values.
GatkReport file Report file output by Genome Analysis Toolkit (GATK).
GenePixDirectory directory GenePix input directory.
GFF file General Feature Format (gene-finding format, generic feature format, GFF) is a file format used for describing genes and other features of DNA, RNA and protein sequences.
GTF file GTF stands for Gene transfer format.
IlluminaDirectory directory Illumina input directory for Illumina BeadStudio output files.
IntervalList file A list of genomic intervals used e.g. in Genome Analysis Toolkit.
LatexList directory List of LaTeX files, not necessarily belonging to the same document.
MaskList directory A folder of sub-folders containing images numbered from 1.png etc.
MotifSet directory A set of MotifMatch matrices representing nucleotide frequenices.
MRF file Sequence Alignment/Map format closely related to RSEQtools called Mapped Read Format.
Ontology file OBO Flat File.
Properties file A key-value map of strings.
RegionSet file Base type for file formats that store collections of DNA regions.
SAM file Sequence Alignment/Map format for storing aligned short reads.
SequenceSet file Base type for file formats that store sequences.
SNPFreq file This matrix represents biallelic SNPs and their genotype frequencies.
SNPMatrix file This matrix consists of rows of samples and columns of markers.
SRA file NCBI Sequence Read Archive files as defined at NCBI SRA Handbook.
StringList file Sequence of strings (messages) separated by newlines.
TARGZ file Tape archive GNU ZIP file.
TextFile file Plain ASCII text with no particular structure specified.
TopType file The implicit parent type of every other type that does not have a more specific parent type.
VCF multifile Variant Call Format.
WekaClassifier file A classifier that may be used for the data classification.
Wiggle file Stores numeric values associated to DNA regions.
WiggleFolder directory Folder containing wiggle files.
YAML file YAML is a human-readable data serialization language.
YAMLList directory YAML is a human-readable data serialization language.
ZIP file ZIP archive.

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