Fastq.gz files from different lanes

[shregeno8]

I have paired-end Fastq files run on 2 lanes. I am getting an error when I try to run whippet-quant.jl

My command is julia bin/whippet-quant_1.jl ${SAMPLE}_L001_R1_001.fastq.gz,${SAMPLE}_L002_R1_001.fastq.gz ${SAMPLE}_L001_R2_001.fastq.gz,${SAMPLE}_L002_R2_001.fastq.gz --out Whippet/results/${SAMPLE}

but this doesn't work.

What is the right command ?

[timbitz]

You have to merge the fastq files manually first, as with most programs.