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Illumina fastq lane output

When I convert bcl to fastq (with bcl2fastq), by default I get several fastq file by sample AND by lane. For instance :

PAN150427_S17_L001_R1_001.fastq
PAN150427_S17_L002_R1_001.fastq
PAN150427_S17_L003_R1_001.fastq
PAN150427_S17_L004_R1_001.fastq

Is there any reason to not merge all lanes into one by default ? From this workflow http://www.htslib.org/workflow/, it seems they merge fastq lane after alignment. Is it really necessary ?

illumina fastq bcl
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updated by igor igor • written by sacha sacha

2 answers

Keeping them separate allows you to work on the files in parallel speeding things up. You could merge the results files at a later step.

You could use --no-lane-splitting option with bcl2fastq v.2.18.x to get a single file per sample, if you prefer that.

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written by GenoMax GenoMax

Some reasons for not merging:

  • You (and anyone who might later work with your data) always knows how many lanes you ran. Although this may sound ridiculous for those who are keeping good records, it's a recurrent problem for many labs.
  • If one of the lanes failed or had some issues, it's easy to take those sequences out.
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written by igor igor

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