FASTQ versus count matrix: how the starting point changes scope

Starting with reads

FASTQ inputs allow a read-level workflow to be scoped: quality assessment, preprocessing where justified, alignment or quantification and downstream analysis. Exact stages depend on the assay, organism, references and design.

Starting with counts

A gene count matrix begins downstream of read processing. Supply sample metadata and how counts were generated, including reference and annotation. A matrix cannot by itself establish that reads were suitable or sample identities were correct.

Counts are not interchangeable

DESeq2 expects suitable unnormalized counts with the relevant sample information and design. TPM, FPKM and transformed expression values are not direct substitutes for raw count input. Quantifier imports require an appropriate documented route.

What the quote needs

State the starting files, their provenance, number of samples, comparisons and expected outputs. Separate any rerun of upstream processing from downstream interpretation. Discuss whether original reads remain available if QC questions arise.

Limitations

This guide describes planning for a common bulk RNA-seq setting. Other assays and statistical methods have different input assumptions. Choose methods with a study-specific review.

Reference and next step

Editorial planning guide prepared by ANGSUMI; this is not a report of original research or a claim of independent scientific review.

Read the underlying method documentation or research guidance

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