I have 6 RNA-Seq samples (same condition,biological replicates). I used tophat and cufflinks to analysis the samples. How to get an 'average' gene expression levels of this replicates?
Can I run cuffmerge on assembly files (transcript.gtf) or first I have to merge 2 accepted_hits.bam files by samtools and then run cufflinks on the merged file?
Can cuffmerge give reasonable FPKM values, and if it can not, how to get an 'average' gene expression levels for biological replicates ?