Prepare Data for Bioinformatics Analysis
Prepare your data
Organize the study information before transferring data. The templates below support the initial project review; analysis-specific file requirements are agreed separately.
Download preparation checklist ↓
Start with the biological samples
- Use a stable sample ID to link files, matrices and metadata.
- Record which samples come from the same biological unit, donor or subject.
- Document condition, batch, pairing, timepoints, pooling and controls where relevant.
- Keep original data and a record of any filtering or processing already performed.
Genomics & variants
- Organism, sequencing assay, platform and sample identifiers.
- Sequencing reads or existing alignment/variant files for review; reference assembly and any vendor reports.
- Study groups, relatedness or pairing where relevant, and the biological question.
Transcriptomics
- Reads or a count matrix with gene identifiers and processing history.
- A sample sheet linking every matrix column or file to its biological sample.
- Condition, batch, biological unit, pairing and relevant covariates; organism and reference information.
Microbiome & metagenomics
- Amplicon or shotgun assay, platform, marker region if applicable, and organism/environment context.
- Read files and processing history; sample metadata and available negative or positive controls.
- Experimental groups, biological units, pooling, collection sites and batches where relevant.
Single-cell analysis
- Count matrices or processed objects for review, with processing history and cell/gene identifiers.
- Sample and donor identifiers, condition, platform, chemistry and batch information.
- Organism, assay and annotation references; raw versus filtered matrix status.
How to use the CSV templates
Each file contains a header row only. Add one row per submitted data record, retaining the biological-unit identifier. If a sample has multiple files or libraries, describe that relationship explicitly. Use a consistent missing-value convention and explain it in your brief.
Fields such as timepoint, donor, marker region and chemistry apply to specific study types. Add study-specific covariates as extra columns. File columns can contain filenames for planning; do not put passwords or private download links in the sheet.
Core field dictionary
| sample_id | Unique label for the submitted sample or library record. |
|---|---|
| biological_unit_id | Independent organism, participant or experimental unit; repeated records retain this identity. |
| condition | Experimental group or condition as defined by the study. |
| batch | Known processing or sequencing batch. |
| file_1 / file_2 | Associated filenames. These fields are not a required paired-end format. |
| notes | Explain pooling, previous processing, missing values and unusual records. |
Before transferring files
Confirm the file inventory, access permissions and transfer method during consultation. Begin with study information and filenames, rather than sending identifiable data or confidential research files through a public enquiry.
Prepare your brief ↗