DataType

alignments

Sequencing reads mapped to positions in a reference genome, typically in BAM/CRAM format with mapping quality scores and alignment coordinates.

→ sequencing reads

alignments with modifications

Aligned reads preserving base modification information (e.g., methylation from bisulfite-seq or direct detection) encoded in BAM auxiliary fields.

diploid personal genome alignments

Reads aligned to a diploid personal genome reference including both parental haplotypes, enabling allele-specific analysis.

gene alignments

Reads or sequences aligned at the gene level.

preprocessed alignments

Alignments after preprocessing: duplicate marking, base quality score recalibration, or indel realignment.

reads

Raw or minimally processed sequencing reads in FASTQ format, including quality scores and read identifiers.

redacted alignments

Alignments with sensitive genomic positions masked or removed for privacy protection in controlled-access data sharing.

redacted transcriptome alignments

Transcriptome-level alignments with sensitive positions redacted.

rejected reads

Reads that failed quality control filters and were excluded from downstream analysis.

spike-in alignments

Reads aligned to exogenous spike-in control sequences (e.g., ERCC) for normalization and quality assessment.

transcriptome alignments

Reads aligned to a transcriptome reference (cDNA sequences) rather than the genome.

→ gene expression, splicing

HMM predicted chromatin state

Chromatin state annotations (e.g., ChromHMM) predicted by hidden Markov model from histone marks.

read annotations

Per-read annotations of alignment features or classifications.

semi-automated genome annotation

Genome annotation produced by a combination of automated and manual methods.

sequence alignability

Track indicating mappability of sequences to the reference genome.

sequence uniqueness

Track indicating uniqueness of k-mer sequences across the genome.

consensus DNase hypersensitivity sites

DNase I hypersensitivity sites consistently identified across multiple samples or cell types.

DHS peaks

Peak calls from DNase I hypersensitivity sequencing (DNase-seq), indicating open chromatin regions.

→ open chromatin regions, footprints

DHS regions reference

Reference set of DNase I hypersensitivity regions.

FDR cut rate

False discovery rate-controlled cut rate signal from DNase-seq analysis.

hotspots

Broad regions of elevated DNase cleavage activity representing domains of chromatin accessibility.

→ open chromatin regions

hotspots1 reference

Reference hotspot calls at lenient threshold (hotspot1 algorithm).

hotspots2 reference

Reference hotspot calls at stringent threshold (hotspot2 algorithm).

nuclease cleavage frequency

Per-base frequency of DNase I or Tn5 transposase cleavage across the genome.

nuclease cleavage corrected frequency

Bias-corrected per-base nuclease cleavage frequency.

contact matrix

Genome-wide matrix of chromatin interaction frequencies from Hi-C or similar chromosome conformation capture experiments.

→ chromatin loops, TADs, compartments

pairs

Raw read pair data from Hi-C or proximity ligation before matrix construction.

variants contact matrix

Contact matrix incorporating variant information.

fold over change matrix

Matrix of fold-change values relative to control across features.

sparse gene count matrix

Sparse matrix of gene-level read counts across cells or samples, standard for single-cell RNA-seq.

sparse peak count matrix

Sparse matrix of peak accessibility counts across cells, used in single-cell ATAC-seq.

sparse transcript count matrix

Sparse matrix of transcript-level counts across cells or samples.

TF peaks matrix

Matrix of transcription factor peak counts across samples.

z scores matrix

Matrix of z-score normalized values across features and samples.

sparse splice junction count matrix

Sparse count matrix of splice junctions.

signals matrix

Matrix of signal values across features and samples.

element barcode mapping

Mapping of element barcodes used in CRISPR screen experiments.

gRNAs

Guide RNA sequences used in CRISPR screens.

guide locations

Genomic locations targeted by guide RNAs.

guide quantifications

Abundance quantifications of guide RNAs from screen data.

non-targeting gRNAs

Guide RNAs designed as non-targeting negative controls.

perturbation signal

Phenotypic signal associated with CRISPR perturbations.

ranked gRNAs

Guide RNAs ranked by screen performance or activity.

reporter code counts

Count data from reporter codes in CRISPR screen readouts.

safe-targeting gRNAs

Guide RNAs targeting genomic safe-harbor loci as controls.

sparse gRNA count matrix

Sparse count matrix of guide RNA abundances across cells.

bias models

Trained models capturing sequencing bias patterns based on sequence composition.

counts sequence contribution scores

Per-nucleotide importance scores explaining sequence contribution to predicted counts (e.g., DeepLIFT, integrated gradients).

DNN-MPRA contribution scores

Nucleotide contribution scores from a deep neural network trained on MPRA data.

DNN-MPRA predicted signal

Regulatory activity signal predicted by a DNN trained on MPRA data.

model performance metrics

Evaluation metrics (AUC, correlation, etc.) assessing predictive model performance.

models

Trained computational or machine learning models saved for prediction or interpretation.

motif model

Sequence motif model (e.g., convolutional filter weights) from deep learning or motif discovery.

profile sequence contribution scores

Per-nucleotide importance scores explaining sequence contribution to predicted signal profiles.

promoter prediction model

Computational model trained to predict promoter activity from sequence.

selected regions for bias-corrected predicted signal profile

Genomic regions selected for bias-corrected signal profile interpretation.

selected regions for count sequence contribution scores

Genomic regions selected for count contribution score analysis.

selected regions for predicted bias profile

Genomic regions selected for predicted bias profile interpretation.

selected regions for predicted signal and sequence contribution scores

Genomic regions selected for combined signal and contribution score analysis.

selected regions for predicted signal profile

Genomic regions selected for predicted signal profile interpretation.

selected regions for profile sequence contribution scores

Genomic regions selected for profile contribution score analysis.

TF binding prediction model

Deep learning model predicting transcription factor binding from DNA sequence.

training and test regions

Genomic regions designated for model training and held-out evaluation.

training set

Data used to train a computational or machine learning model.

bidirectional peaks

Peaks from bidirectional transcription signal, characteristic of active enhancers and promoters.

→ enhancers, promoters

conservative IDR thresholded peaks

Peaks using a conservative (stricter) IDR cutoff, yielding high-confidence but smaller peak set.

→ TF binding sites, open chromatin regions

distal peaks

Peaks located distal (>2-3kb) from transcription start sites, often representing enhancers.

divergent peaks

Peaks from divergent transcription where initiation occurs in both directions from a central point.

IDR ranked peaks

Peaks ranked by IDR score, with lower IDR indicating higher reproducibility across replicates.

optimal IDR thresholded peaks

Peaks using the optimal IDR cutoff balancing sensitivity and reproducibility.

→ TF binding sites, open chromatin regions

peaks

Discrete genomic regions of statistically significant enrichment from peak calling. The fundamental unit of ChIP-seq and ATAC-seq analysis.

→ TF binding sites, open chromatin regions, histone modifications, enhancers

peaks and background as input for IDR

Combined peak and background signal data formatted as input for IDR analysis.

proximal peaks

Peaks located proximal (<2-3kb) to transcription start sites, often representing promoters.

pseudoreplicated IDR thresholded peaks

IDR-thresholded peaks from pseudoreplicates (subsampled reads) when true replicates unavailable.

pseudoreplicated peaks

Peak calls from pseudoreplicates created by subsampling reads from a single experiment.

replicated peaks

Peaks reproducibly called across biological or technical replicates.

→ TF binding sites, open chromatin regions, histone modifications

representative DNase hypersensitivity sites

A curated representative set of DNase hypersensitivity sites for reference.

representative IDR thresholded peaks

A representative set of IDR-thresholded peaks selected for downstream analysis.

unidirectional peaks

Peaks from unidirectional transcription signal, typically associated with gene bodies.

valleys

Local minima in signal tracks used in footprint detection or nucleosome positioning analysis.

differential expression quantifications

Statistical results from differential expression analysis comparing conditions.

differential splicing quantifications

Statistical results from differential splicing analysis comparing conditions.

element quantifications

Quantification values for regulatory elements.

exon quantifications

Read counts or expression values quantified at individual exons.

→ exon usage, splicing

gene quantifications

Expression quantifications at gene level as read counts, TPM, or FPKM values.

→ gene expression

gene stabilities

Measurements of mRNA or gene expression stability over time.

genic features quantifications

Quantifications across various genic features (exons, introns, UTRs).

genic regions quantifications

Read count quantifications over defined genic regions.

merged transcription segment quantifications

Quantifications from merged transcription segments.

microRNA quantifications

Expression quantifications of microRNAs (miRNAs).

mRNA stabilities

Measurements of mRNA half-life or decay rates.

novel peptides

Peptides identified that are absent from reference databases.

peptide quantifications

Abundance measurements of peptides from mass spectrometry proteomics.

protein expression quantifications

Abundance measurements of proteins from proteomics data.

scaled RNA stability

RNA stability measurements scaled across samples.

transcript quantifications

Expression quantifications at transcript isoform level.

→ transcript expression, splicing

transcribed region quantifications

Quantifications over transcribed genomic regions.

transcription segment quantifications

Quantifications over discrete transcription segments.

UV enriched segment quantifications

Quantifications from UV-crosslinking enriched RNA segments.

modified peptide quantification

Quantification of post-translationally modified peptides.

chromosome sizes

File listing chromosome/contig names and lengths, required by many genomics tools.

chromosomes reference

Reference sequences for individual chromosomes.

elements reference

Reference set of annotated genomic elements.

genome index

Precomputed index enabling rapid sequence alignment to a reference genome.

genome reference

Reference genome sequence assembly used for alignment and annotation.

miRNA reference

Reference sequences and annotations for microRNAs.

mitochondrial genome index

Alignment index for the mitochondrial genome.

mitochondrial genome reference

Reference sequence for the mitochondrial genome.

motif clusters reference

Reference set of clustered sequence motifs.

phastcons score reference

Reference phastCons conservation scores across the genome.

reference

Generic reference data file.

repeats reference

Reference annotations of repetitive elements.

rRNA reference

Reference sequences for ribosomal RNA.

snRNA reference

Reference sequences for small nuclear RNA.

transcriptome index

Index for rapid alignment to transcriptome reference sequences.

transcriptome reference

Reference transcript sequences for a species, used for RNA-seq alignment.

tRNA reference

Reference sequences for transfer RNA.

enhancer prediction model

Model predicting enhancer activity from sequence or chromatin features.

regulatory elements prediction model

Computational model for predicting regulatory element activity and location.

base overlap signal

Signal computed from base-level read overlap counts at each genomic position.

bias-corrected predicted signal profile

Model-predicted signal after correction for sequence-composition bias.

control normalized signal

Signal normalized against a matched control experiment to remove background and technical artifacts.

enrichment

Quantitative enrichment score over background, measuring signal above expected noise level.

fold change over control

Signal expressed as the ratio of experimental signal to input/control, highlighting enrichment over background.

→ TF binding, histone modifications

signal

Quantitative signal track showing per-base or per-bin values across the genome, typically in bigWig format.

→ gene expression, chromatin accessibility, TF binding

signal p-value

Statistical significance track showing -log10(p-value) of enrichment at each position.

summed densities signal

Signal computed as the sum of per-base read densities across the region.

wavelet-smoothed signal

Signal smoothed using wavelet transform to reduce noise while preserving peak structure.

end position signal

Signal of read end positions.

signal profile

Signal profile across genomic positions.

bias profile

Sequencing bias profile across genomic positions.

control profile

Control signal profile.

archr project

ArchR software project file with processed single-cell ATAC-seq data and analyses.

cell coordinates

Low-dimensional coordinates (UMAP, t-SNE, PCA) for single-cell visualization.

cell topic participation

Cell-level participation scores in latent topics from topic modeling.

clusters

Cell cluster assignments from unsupervised clustering of single-cell data.

capture targets

Genomic regions targeted for enrichment in capture-based sequencing (exome, panels).

exclusion list regions

Genomic blacklist regions excluded due to mapping artifacts or technical issues.

filtered regions

Genomic regions removed from analysis after filtering.

fragments

DNA or RNA fragment data prior to alignment.

idat green channel

Green channel intensity data from Illumina IDAT microarray files.

idat red channel

Red channel intensity data from Illumina IDAT microarray files.

inclusion list

Allowlist of genomic regions or barcodes included in analysis.

index reads

Index read sequences for sample demultiplexing.

intensity values

Raw intensity measurements from microarray or imaging experiments.

kmer weights

Frequency or weight values for k-mer sequences.

library fraction

Proportion of sequencing library represented by a sample or subset.

mitochondrial exclusion list regions

Mitochondrial regions excluded from nuclear genome analysis.

nanopore signal

Raw ionic current signal from nanopore sequencing.

negative control regions

Genomic regions used as negative controls in experiments.

positive control regions

Genomic regions used as positive controls in experiments.

primer sequence

Oligonucleotide primer sequences used in PCR or sequencing.

R2C2 subreads

Rolling circle amplification sub-reads from R2C2 long-read sequencing.

raw data

Unprocessed experimental data in original format before computational processing.

raw imaging signal

Unprocessed signal from imaging-based experiments.

sequence adapters

Adapter sequences ligated to library fragments for sequencing platform compatibility.

sequence barcodes

Short DNA sequences labeling samples (multiplexing) or individual cells (single-cell).

spike-ins

Exogenous sequences of known concentration added for normalization (e.g., ERCC RNA spike-ins).

subreads

Sub-read data from long-read sequencing platforms (PacBio).

validation

Data generated for experimental validation purposes.

fine-mapped variants

Variants identified as likely causal through statistical fine-mapping within associated loci.

variant functional prediction

Computational predictions of variant functional impact.