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Question: Reference Genome how does it validate
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gravatar for premraj.preeti
8 days ago by
premraj.preeti • 10
premraj.preeti • 10 wrote:

I have a very basic question. We map the m-RNA sequence cDNA with the reference genome and then based on the alignment of the reads figure out of which of the genes were expressed. But when reference genome was created I understand that it is iterated continuously to map the best possible genome.

But no genome can be perfect that can be referred. So if we are mapping a cdna and saying that the gene is deferentially expressed, it is quite possible that the reference genome has a snp and the read under consideration is correct.

I am confused with this whole reference genome mapping. Can someone help me get a more clear picture
genome • 31 views
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modified 7 days ago by Jennifer Hillman Jackson ♦ 25k • written 8 days ago by premraj.preeti • 10
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gravatar for Jennifer Hillman Jackson
7 days ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It is true that a reference genome can contain variation. It is difficult to define what is the "most common allele" (snp), especially for organisms that may have a different "most common allele" for different sub-populations. This is also true for more complex genomic sequence rearrangements (mnps, indels). An assembled genome is a standardize base-line reference sequence that data can be compared against.

What is important for most analysis, including differential expression analysis, is to compare all of your data to the same exact reference genome (or transcriptome/exome). That way expression differences between samples/conditions that are present in your data are all based on the same underlying sequence, the "reference" sequence. Data mapped to the same reference can be compared to each other and to other features mapped to that same reference.

It may help to review some of the Galaxy tutorials to get a better understanding of how reference sequence (and annotation) are used in an analysis. Most tutorials include links to external publications and help guides, along with summary descriptions about what is going on scientifically behind the technical steps performed during an analysis.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 7 days ago by Jennifer Hillman Jackson ♦ 25k

Thanks for the explanation

ADD REPLY • link written 7 days ago by premraj.preeti • 10
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