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 . 


Indexing a genome can be explained similar to indexing a book. If you want to know on which page a certain word appears or a chapter begins, it is much more efficient/faster to look it up in a pre-built index than going through every page of the book until you found it. Same goes for alignments. Indices allow the aligner to narrow down the potential origin of a query sequence within the genome, saving both time and memory.

You may have a look at Ben Langmeads youtube channel (creator of the bowtie and bowtie2 alignment software), where he lectures about concepts of sequence alignments, including the idea of indexing.

https://www.youtube.com/user/BenLangmead