Extract text from gene count files (COUNT)
To convert COUNT count files 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 .count file is primarily a gene expression read count matrix generated by HTSeq (specifically the htseq-count tool), a Python-based software suite used in bioinformatics and computational biology. These files store the raw quantification of how many sequencing reads map to specific genomic features (genes, exons) in RNA-Seq experiments. Internally, the file is a simple tab-delimited text format containing two columns: the Feature ID (e.g., ENSG00000139618) and the integer Count (e.g., 2543).
The main issue for researchers and students is that .count is not a standard system extension. Windows and macOS treat it as an unknown file type, refusing to open it on double-click. While it can be opened with a text editor like Notepad++, users typically need to analyze this data in spreadsheet software like Microsoft Excel or statistical environments like R. Opening it directly in Excel often results in formatting errors where columns are merged or headers are missing. Additionally, these files contain special metadata rows at the bottom (like __no_feature or __ambiguous) that can break downstream analysis if not properly filtered. Converting your .count file to CSV or XLSX ensures the data is correctly structured with headers, making it immediately ready for tools like DESeq2 or edgeR.
Convert.Guru analyzes your COUNT file, detects the exact format, and lets you read the text inside.
If you want to convert COUNT file to CSV, JSON, XML, YAML, YML, TOML, INI, CFG, CONF, DAT, DB or SQL, 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 COUNT, 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 COUNT converter.