mapping

[zhangleigloria]

Dear sir,
I'm sorry to bother you, and I want to ask you a question. I have a sample which has four line data, such as L1.1.fq.gz, L1.2.fq.gz,L2.1.fq.gz, L2.2.fq.gz,L3.1.fq.gz, L3.2.fq.gz,L4.1.fq.gz, L4.2.fq.gz. When I run the first step (for mapping), do I need to map them separately (-1 L1.1.fq.gz -2 L2.1.fq.gz) ? After get the bam file ,should I merge with them using samtools merge? Or put all *.1.fq.gz files under one path and *.2.fq.gz under another path.
Could you help me with the answer?
best wish