As i am from non biological background, I have a basic question regarding the reference genome used for read alignment of DNA and RNA seq data. Are they different or same??
1st of all DNA = nucleotide and RNA = transcripted DNA so there are different alignments conclusion is references are different for DNA and RNA
No of course not! You need to keep in mind that the sequencer does not distinguish between samples coming from transcriptom or DNA, therefore, you will always get T,C,G,A bases in your bam. It is you who knows those sequences are RNA.
Therefore, the reference is applicable to both. The interpretation is different in the downstream anaylsis.
That's true. Nevertheless, you should use different alignment tools for DNA-Seq and RNA-Seq. As Dan wrote above, with RNA-Seq you'll need to detect splice junctions. Also the quality parameters which are crucial for DNA-Seq don't need to be as crucial using RNA-Seq data (e.g. sequence duplication, GC-bias, ...), since these factors can be introduced by the transcript abundances.
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Just to clarify RNA is not equal to protein. RNA is transcribed DNA. Then some RNA transcript can be translated into protein. But you are right to say that alignment approach are different regarding DNA or RNA sequencing
As i read DNA-Seq has ATCG, and RNA-Seq has AUCG. If i need to align an RNA read with reference genome , can i use the reference genome of DNA containing combinations of ATGC only having no U present. I am confused!!
There is no U in RNA-Seq libraries as the sequencer used the cDNA (not the RNA) to sequence. So use the reference genome to align. FYI a genome is always DNA (not RNA). You should read some review paper on RNA-Seq before doing any analysis. It's important to understand the underlined method.
So can i conclude that i can use genome reference containing combinations of ATCG to align both DNA and RNA seq reads.
yes you can use the reference genome for both data
To add to this, usually in RNA-Seq experiments you use the reference genome but you also use some sort of transcript reference (if available for your organism) to give prior information about transcripts, splicing, etc. If working with a totally novel transcriptome of course this doesn't apply.