Preflight checks (QC)

  • Updated

Tapestri DNA Pipeline starts with running a quality check (QC) module, which checks the validity of the input data. This QC module ensures that the FASTQ files used are valid and have no issues that might cause DNA Pipeline to fail. It also detects the chemistry and sets it as the run chemistry for the downstream analysis of the DNA Pipeline. If all files pass QC, DNA Pipeline moves on to the next step.

DNA Pipeline uses the fastp module to perform the quality checks.

Failure of QC

Under certain conditions, the QC may fail, and in every event, the run status displays a suitable message. The following table summarizes the errors along with the run status and reason for the error.


Run Status


QC failed due to FASTQ file corruption

QC Failed

  • FASTQ file is not a valid .gz archive.

A sample is oversequenced

Oversequenced Sample

  • The expected coverage for the FASTQ file containing the reads is more than 320x, where
    expected_coverage = (read_count * tube_count * lane_count) / (expected_num_of_cells = 20000 * amplicon_count)

QC failed due to high percent of Ns at a position

QC Failed

  • The positions with max Ns in R1 or R2 contain more than 20% Ns.

Could not detect chemistry

QC Failed

  • Fixed part counts for V1 and V2 chemistries are insufficient to reliably determine the chemistry of the sample.

Panel zip file is not correct

  • The panel file does not have the correct structure. See more details about the zip folder structure.

Based on the reasons above, investigate the reason for the run failure or contact for additional help.

Share this article:

Was this article helpful?

2 out of 2 found this helpful

Have more questions? Submit a request