Downloadable · coming soon
Cell Ranger FASTQ filename renamer
cellranger count looks for [Sample]_S#_L###_R#_001.fastq.gz. A dot in the sample prefix, a missing lane token, or an NCBI-style _1.fastq.gz name is enough for the pipeline to skip the files even when the reads are fine. A mapping CSV does not finish that job—the files on disk still have the wrong names.
For core-lab staff and analysts who were just told the FASTQs are missing, and who need a program that will rename the run folder after they inspect the plan.
How it works
01
Download the program
Install a small executable for macOS, Windows, or Linux. Sequence files are not uploaded.
02
Point it at the FASTQ folder
The program reads filenames in that directory. It does not open, gzip, or transmit the reads.
03
Review the plan
See which names already match Cell Ranger, which have a deterministic syntax repair, and which need a human look because the layout was inferred.
04
Apply safe renames
Confirmed syntax repairs are applied in the folder. Inferred names (for example SRA _1/_2) stay unchanged until you accept them. A mapping and versioned record are written beside the run.
Constraints and checks
- Illumina names with and without a lane token (Cell Ranger v4+)
- Dots, spaces, and other illegal characters in the sample prefix
- .fq.gz → .fastq.gz and unpadded L1 → L001
- Common SRA/NCBI _1/_2 layouts, flagged for review and not renamed until you confirm
- Missing R1/R2 coverage per sample prefix
- In-folder rename of unambiguous syntax errors, plus a mapping you can keep
What it will not do
- It is not a browser checker. Renaming a run folder requires a local program.
- It does not open, gzip, or upload FASTQ contents.
- It will not invent a read type when the name does not contain one.
- It does not run cellranger or check FASTQ headers, quality, or chemistry.
- BCL Convert sample sheets are a separate destination and are not included here.
Why this failure happens
- Why Cell Ranger misses FASTQs with a dot in the sample prefix
Cell Ranger splits Illumina FASTQ names on a period. A dot inside the sample prefix makes --sample miss valid reads. How to see it, and how to repair the name without touching sequence.
- Rename SRA FASTQ names for Cell Ranger
fastq-dump writes SRR…_1.fastq.gz. Cell Ranger wants an Illumina suffix. The mapping is usually R1/R2, but three-file dumps exist, so the planned renamer proposes a name and does not apply it until you confirm read identity.
Trust, files, and price
- Planned as a free download
- Runs on your machine; sequence files never leave it
- Ambiguous repairs are labeled needs-review and are not applied until you say so
- No patient-identifiable data by design
Planned as a free downloadable for macOS, Windows, and Linux. No account.
Get notified when the download is ready
No account is created. We will only use this address to tell you when the program can be downloaded.
Questions
- Why do dots in the sample name break Cell Ranger?
- Cell Ranger splits the Illumina suffix at '.'. If the sample prefix itself contains a dot, the file no longer matches [Sample]_S#_L###_R#_001.fastq.gz and --sample will not see it. Replacing those dots with underscores is the usual repair.
- Why a downloadable instead of a web page?
- The job is to change filenames in the run folder. A browser can show you the mapping; it cannot apply the rename. The program prints a plan, applies safe syntax repairs, and leaves inferred layouts untouched until you confirm them.
- What about NCBI SRA downloads?
- Names like SRR9291388_1.fastq.gz are a common layout, not the Illumina convention. We propose SRR9291388_S1_L001_R1_001.fastq.gz and mark it for review, matching 10x’s published SRA guidance. That rename is not applied until you accept it.
- Is this free?
- Yes. The renamer is planned as a free download. FASTQ contents are never read or uploaded.