I want to ask a basic question because this is the first time I try RNA-seq analysis. My original task is basically to count several genes transcription level. I have 8 aligned RNA-seq data with Tophat. There are 2 categories, normal and disease. For Normal I give number 34,35,36, and 37. For Disease I give number 41,42,43, and 44. I already get the aligned bam file from tophat and I follow some workflows to use cufflinks to generate gtf file for each data. I have done that and I also finished merge all 8 data with cuffmerge. Basically, I follow the diagram flow for cufflinks >=2.2 from here : http://cole-trapnell-lab.github.io/cufflinks/manual/
For human GTF file, I download from : http://genome.ucsc.edu/cgi-bin/hgTables?command=start
I'm a bit confused with the step after that. After I use cuffmerge, I get 1 GTF file and then the step after is cuffquant. What is the input of this cuffquant? The graph said final transcriptome assembly and mapped reads, but which mapped reads? Is it the original accepted_bam from Tophat?
Thank you for your answer.