What are the QC error messages?

  • Updated

QC failed due to FASTQ file corruption

  • FASTQ file is not a valid vcf.gz archive,
  • FASTQ info file contains error messages, or
  • FASTQ file is incomplete, corrupted either during download from the sequencer or during the upload to the DNA Pipeline account.

Sample is oversequenced

The expected coverage for the FASTQ file containing the reads is more than 320x, based on the following formula:

expected_coverage = (read_count * tube_count * lane_count) / (expected_num_of_cells = 20,000 * amplicon_count)

QC failed due to a high percentage of Ns at a position

The position max Ns in R1 or R2 contains more than 20 % Ns. ā€œNā€ replaces ATGC when the software is unable to make a base call for a position.

Could not detect chemistry

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

Read more about the error detection process.

QC failed due to invalid protein panel

  • Name, ID or Sequence columns are missing in the panel file. 
  • Sequence column contains non-ATGC characters.
  • Duplicate barcodes, same barcode is present more than once, duplicate name or IDs.
  • Panel file contains empty lines, which is also represented by invalid barcode. Use a text editor like Notepad, TextEdit etc to open the file and check there are no lines with only commas. This is not visible in Excel or Excel like tools.


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