Opened 2 years ago

Closed 2 years ago

#1431 closed enhancement (fixed)

More validation of library barcodes

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.41.3
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

We discovered a case where the specified barcode in the Library section didn't match the sequencing cycles setting in the flow cell section.

The library was specified to use a 8+8 bases barcode while the sequencing cycles used x-10-10-x indicating a 10+10 bases barcode. The header in the FASTQ file also had the 10+10 bases barcode.

It should be possible to implement a validation for this.

  1. Check that both FASTQ files have the same barcodes. NOTE! There may be reading error so some mismatches should be allowed.
  2. Check that the length of barcode that is specified for the library item matches the sequencing cycles specification
  3. Check that the barcode sequences that are specified for the library item matches the FASTQ files. NOTE! There may be reading error so some mismatches should be allowed. NOTE 2! The second barcode is reverse-complemented in the FASTQ file.

Change History (1)

comment:1 by Nicklas Nordborg, 2 years ago

Resolution: → fixed
Status: new → closed

In 6956:

Fixes #1431: More validation of library barcodes

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