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10x Genomics
Chromium Single Cell Immune Profiling

FASTA/FASTQ Files

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.

Quality Scores

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.