CASAVA combine samples across all lanes

[id0]

By default, when demultiplexing with CASAVA, same sample across multiple lanes is added to separate FASTQ file for each lane. Is there a way to have one FASTQ file for each sample?

There is a --fastq-cluster-count option so that FASTQs are not limited to a certain amount of reads. Maybe there is something to make FASTQs not limited to one lane?

[kmcarr]

Nope, this is not possible with CASAVA. You'll have to settle for taking the per lane FASTQ from CASAVA and concatenating them after the fact.

[sphil]

which shouldn't be a problem since you can use cat on every unix OS for that...