Cell Ranger4.0, printed on 12/26/2024
The cellranger vdj pipeline outputs several indexed FASTA and FASTQ files.
| File type | Primary Use Cases |
|---|---|
| FASTA | Downstream tools such as the Integrated Genome Viewer (IGV) or V(D)J annotation tools like IGBLAST. |
| FASTQ | Inspecting assembly base quality scores |
| File | Records | Description |
|---|---|---|
| filtered_contig.fasta | Assembled contigs | High-confidence contig sequences in cell barcodes. |
| filtered_contig.fastq | Assembled contigs | High-confidence contig sequences in cell barcodes. |
| all_contig.fasta | Assembled contigs | All assembled contig sequences. |
| all_contig.fastq | Assembled contigs | All assembled contig sequences. |
| consensus.fasta | Clonotype consensus sequences | Clonotype consensus sequences. |
| consensus.fastq | Clonotype consensus sequences | Clonotype consensus sequences. |
| concat_ref.fasta | Concatenated germline segments | Concatenated V(D)J germline segments for the segments detected on each consensus sequence. These serve as an approximate reference for each consensus sequence. |
Typically, quality scores in a FASTQ file indicate the Phred-encoded probability that the base is correct. When a FASTQ file contains records for sequencing reads, the quality scores usually indicate the confidence of the base-caller at each base. Because cellranger vdj produces quality scores for assembled bases, the interpretation is slightly different.
| File | Interpretation |
|---|---|
| filtered_contig.fastq | Probability that the base is not a sequencing, PCR, or reverse-transcription (RT) error. The quality score is computed using the per-read sequencing Q-scores and an assumed RT error rate. |
| all_contig.fastq | Same as above. |
| consensus.fastq | Same as above, except the reads used to assemble all of the contigs used to produce the consensus are used. |