Question: Questions about Reference Sequence in DESeq2
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gravatar for williamsbrian5064
2.6 years ago by
williamsbrian5064250 wrote:

I am trying to use Geneious to do some expression analysis using Dseq2. I was going through the tutorial and the reference sequence they used was super complete (NC_006841). It was annotated and it had the name of the proteins, min, max, length, and direction. I'm just wondering where they even got that reference sequence from? The best I can get is just a fasta file with the genome. I'm working with Drosophila so I was guessing there is a reference sequencing out similar to the one they used in their tutorial. (https://www.geneious.com/tutorials/expression-analysis-deseq2/)

Would it be under "Assembly" on NCBI nucleotide?

ADD COMMENTlink modified 2.6 years ago by h.mon30k • written 2.6 years ago by williamsbrian5064250

Which Drosophila? Did you look at Flybase?

ADD REPLYlink written 2.6 years ago by h.mon30k

Drosophila Melanogaster. I've looked at flybase but I'm not entirely sure what kind of file I'm looking for? They didn't explain much in the tutorial.

ADD REPLYlink written 2.6 years ago by williamsbrian5064250

Contact Geneious tech support since you have a license for the software. They can tell you where the annotations came from.

ADD REPLYlink written 2.6 years ago by genomax85k

I just don't think mapping the RNA-seq reads to a Drosohpilia reference will tell me much about expression. I feel like I'm missing something here.

ADD REPLYlink written 2.6 years ago by williamsbrian5064250
0
gravatar for h.mon
2.6 years ago by
h.mon30k
Brazil
h.mon30k wrote:

I can't help you with Geneious, as I don't use it - so far, I haven't even been able to pronounce its name, so I pretend it don't exist. There are several detailed workflows and tutorials out there (one example, among many, here), but generally speaking, you have to:

1) map your sequencing reads to a reference genome or transcriptome

2) summarize read counts using an annotation

3) perform differential expression analysis

Flybase has a very complete D. melanogaster genome and annotation, but it should be the same or very close to those from Ensembl or NCBI.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by h.mon30k
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