Im using tophat protocol so now my step one is done I have set of 4 bamfles.Now according to the protocol the next step is to run the cufflinks using the generated bam files , how can I run cufflinks from multiple bam files ,can anyone help me how do I do that ?Im not sure if its going to reduce my execution time or not but it will help me to do other stuff at the same time I suppose .
Those 6 are from the same sample or multiple samples?
Sorry its 4 bam files , my mistake, so Sample 1 and its replicate which is control and Sample 2 and its replicate which is my test sample. so in total i have 4 bam files