Hi all

Though tophat uses bowtie in mapping, what is the specific use of tophat in rna seq. can someone also highlight me the importance of other software modules such as cufflinks, cuffdiff and cuff merge in rna seq

it is often said, that rna-seq is useful in analyzing gene expressions, but i feel that small changes in mrna expression would also lead a huge amounts of protiein in a cell and hence, how do we reduce this bias. I also heard that a method known as gene enrichment analysis exist for reducing this bias, can we do it using pipeline pilot