Hello guys
  I'm working on Rna SEQ data, and I want to get good conceptual knowledge about the analysis of the process. 

I used the tool bowtie for indexing my reference genome and then the rest is according to the TUXEDO pipeline.

I don't understand what exactly, "indexing" of the reference genome is and why it had to be done.

I do get the point that there are many genes that can be identified and can be matched to the genome and indexed, But i am not clear as ti why should we do this , how is it done . ( i am new to bioinformatics and with minimal knowledge  its so hard to understand the algorithm part of it )

so can anyone put it in simple concepts . 


> Such programs as Maq and Bowtie (Table 1) use a computational strategy known as ‘indexing’ to speed up their mapping algorithms. Like the index at the end of a book, an index of a large DNA sequence allows one to rapidly find shorter sequences embedded within it.

Read more from [here][1]


  [1]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836519/