What does term chemistry in the pipeline output files refer to?

  • Updated

The term chemistry in pipeline outputs refers to the barcode version. As seen here both the V2 and V3 chemistry use the V2 version of the barcodes, as a result all the V3 pipeline outputs report the chemistry as V2. Some examples include the qc.json file, it has a chemistry check with output as:

{
"description": "Determine chemistry version based on presence of barcodes in a subset of reads in the FastQ file",
"name": "chemistry",
"status": "passed",
"threshold_warning": 0.5,
"value": {
"detected": "V2",
"read_rates": {
"AGTACGTACGAGTC": 0.953645,
"GTACTCGCAGTAGTC": 0.968625
},
"sample_reads": 200000
}

The log file tapestri_run_output.txt, which mentions the chemistry version:

2023-06-09 03:54:41 Checking system requirements
2023-06-09 03:54:41 Preflight Checks Completed in 20.71s
2023-06-09 03:54:41 preflight checks passed
2023-06-09 03:54:41 Detected chemistry V2
2023-06-09 03:54:41 Barcode Extraction Started
2023-06-09 03:54:41 Running barcode extraction

In all such instances the version refers to barcode version and not the experimental chemistry. There is no way to differentiate V2 or V3 chemistry based on the output files.

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