what is $PU? - Githubissues

bsmn / bsmn-pipeline

BSMN common data processing pipeline

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what is $PU? #21

Open kdaily opened 5 years ago

kdaily commented 5 years ago

https://github.com/bsmn/bsmn-pipeline/blob/master/genome_mapping/job_scripts/aln_1.align_sort.sh#L13

kdaily commented 5 years ago

I think it's 'platform unit'. Is it from the fastq header composed of the {FLOWCELL_BARCODE}.{LANE}.{SAMPLE_BARCODE}?

bintriz commented 5 years ago

You're right. It stands "platform unit" and is extracted from each read name in the fastq while running genome_mapping/job_scripts/pre_2.split_fastq_by_RG.sh. The format here I'm using is "FCX"_L"LN".