Extract text from gene expression files (COUNTS)
To convert COUNTS read counts to another format, you need HTSeq or other Data software.
To convert other file formats to the "Bioinformatics Data" file type, you need software like HTSeq or a similar tool.
A .counts file is the standard output format generated by HTSeq, a Python-based bioinformatics framework used to quantify gene expression in RNA-Seq experiments. These files consist of two tab-delimited columns: a unique gene identifier (Ensembl ID or gene symbol) and an integer representing the raw number of reads mapping to that feature.
While technically plain text, .counts files present significant friction during downstream analysis. A major risk involves opening these files directly in Microsoft Excel; the software frequently misinterprets specific gene symbols (e.g., MARCH1, SEPT1) as calendar dates, silently corrupting the dataset - a widespread issue in genomics known as the 'gene name error.' Furthermore, .counts files are generated individually per sample. Researchers often find themselves with folders containing hundreds of separate files that must be manually merged into a single matrix for analysis in tools like RStudio.
To safely view the data without corruption, convert .counts to CSV or XLSX (ensuring text-formatting for gene columns). For archiving or publication, converting to a standardized TSV or merging multiple files into a single CSV dataset is the recommended workflow to ensure compatibility with differential expression tools like DESeq2 or edgeR.
Convert.Guru analyzes your COUNTS file, detects the exact format, and lets you read the text inside.
Users also converted TFT, BEF, GPX, TPM and CPM files.
If you want to convert COUNTS file to TPM, CPM, CSV, JSON, XML, YAML, YML, TOML, INI, CFG, CONF or DAT, you can use HTSeq or similar software from the "Gene Expression Quantification" category. In the File menu, look for Save As… or Export….
To convert DBF, XML, SQLITE, XLSX, SQL, TSV, ACCDB, YAML, MDB, CSV, ODS or JSON files to COUNTS, try HTSeq or another comparable tool in the "Gene Expression Quantification" category.
The history of Convert.Guru began over 25 years ago in California with Tom Simondi’s file-format database. A former contributor to Space Shuttle development and a software pioneer of the 1980s, Simondi established a trusted resource for file type analysis that was even referenced by Microsoft Windows XP. Today, we use modern technology to process and convert thousands of file formats while continually improving our COUNTS converter.