Question: Illumina fastq lane output
0
gravatar for sacha
2.6 years ago by
sacha1.8k
France
sacha1.8k wrote:

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 ?

bcl fastq illumina • 1.3k views
ADD COMMENTlink modified 2.6 years ago by igor8.7k • written 2.6 years ago by sacha1.8k
3
gravatar for genomax
2.6 years ago by
genomax73k
United States
genomax73k wrote:

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.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by genomax73k
2
gravatar for igor
2.6 years ago by
igor8.7k
United States
igor8.7k wrote:

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.
ADD COMMENTlink written 2.6 years ago by igor8.7k
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