Running with more than one file for left/right reads

[holtgrewe]

In practice, we often have more than one left and right read file as we split experiments over lanes.

What's the best way to call pizzly (and Kallisto) in this case?

[pmelsted]

Run all readfiles from the same sample in a single kallisto command

kallisto quant ... --fusion file1.R1.fastq.gz file1.R2.fastq.gz file2.R1.fastq.gz file2.R2.fastq.gz ...

This is equivalent to cating them to a single file. The pizzly command doesn't change