Hello everyone, i am using some dataset to identify novel transcript during infected condition. I have data as shown in following image (replicates are biological replicates taken from pool of few plants for control and infected separately)
now to analyze using tophat
Procedure 1: one way is to map both replicate of control together and likewise infected together using tophat and get 2 bam files then use these bam files for cufflinks input, get 2 gtf file, 1 for control & 1 for infected, merge them using cuffmerge, use it as for expression quantification and differential expression analysis of 2 bam files.
Procedure 2: other one is map each biological replicate separately using tophat get 4 bam files, use these 4 bam files as input for cufflink, get 4 gtf files, merge them with cuffmerge, use it as for expression quantification of 4 bam files separately and differential expression analysis.
is there any other way to analyze this data and which one of these two procedure should i choose? Problem with procedure 1, I think is during differential expression analysis i will not have replicate for differential expression analysis.