I have 4 lanes in each set of reads. I do understand using the multiple datasets option will run all pairs, but each pair separately.
BUt what I want to achieve is little different -
There is a command line option in bowtie2 where if you give all lanes of R1 as one set of inputs(using option -1) and and all lanes of R2 as another set(using option -2) it will automatically process and provide only one *.bam file as output. Is the similar possible in galaxy?