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" file type, you need software like HTSeq or a similar tool.
The .counts file is a plain-text bioinformatics data format utilized to store raw gene expression read counts. It is predominantly generated by HTSeq, specifically via the htseq-count script, during RNA-Seq analysis pipelines. The file associates biological features, such as Ensembl gene IDs, with integer values representing the total mapped sequencing reads.
The core disadvantage of the .counts format is its unrecognized extension. Standard operating systems lack native file associations for it, forcing users to manually assign text editors or rely on command-line interfaces. Furthermore, these files are often devoid of standard column headers and typically include proprietary diagnostic rows at the EOF (End of File), such as __ambiguous or __not_aligned, which will instantly break standard spreadsheet imports or naive statistical scripts.
To share this data with non-bioinformaticians or explore it in Microsoft Excel, you must convert .counts to standard CSV or XLSX. For downstream analysis in R or Python, standardizing the structure to a clean TSV format is optimal. Just drag and drop your file here to analyze and convert it securely right in your browser.
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 Read Counts" 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 Read Counts" 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.