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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

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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

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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.