Demultiplexing large sequencing runs split amongst multiple output files (multiple R1/R2/R3 .fastq)

[JacobRPrice]

We have a couple of projects where the sequencing facility has given us our results in the form of 50-60 R1, R2, R3 .fastq files. Is there a way to apply idemp to multiple files, ensuring that the output of one set of files ("R1_001.fastq" and "R2_001.fastq") isn't overwritten by the following pair of read files ("R1_002.fastq" and "R2_002.fastq")?

[yhwu]

It only process one set of I1, R1, R2 files at a time. So, to your question, no, it doesn't manage multiple files. You could let it write outputs to different directories with the -o option to avoid files being overwritten. By the way, make sure one of R1, R2, R3 is index read.