Assuming the two lanes are L001 and L002;
#!/bin/bash
raw_data=/path/to/raw_data/
cd ${raw_data}
for f1 in $(ls *L001*); do
for f2 in $(ls *L002*); do
cat ${f1} ${f2} > ${raw_data}merged_files/${f1::(-16)}${f1:48}
done
done
exit
Change ${f1::(-16)}${f1:48} according to sample names.