Hello community, I would certainly appreciate some help here. Many thanks in advance.
I have been looking around about this subject and everything refers to differential expression of RNA-Seq which is a little different from what I am looking for. I am working with a virus and I would like to assess the depth of coverage produced by sequencing their genomes from two different sources (genomes are the same, the sources are different). Even though both sources are quite different the first step after RNA extraction is a OneStep RT-PCR. I mentione this because as you may guest already I usually get a pretty good coverage. The question here is wether those coverages are comparable.
I have 30 samples that were ran in different runs in a Mi-Seq platform. Let's say that half of the samples come from one source and that the other half from the other one. Since I want to compare them what I would like to do is to normalize the dataset. What I have in mind is to normalize by log2 instead of normalizing by total number of reads. Then calculate the Depth of coverage based on the number of reads normalized. Does it make sense? Should I go for DESeq or some other package? I think that at the end I will end up comparing the results using different approaches but I just would like some comments and suggestions.
Thanks once more.
I have been looking around about this subject and everything refers to differential expression of RNA-Seq which is a little different from what I am looking for. I am working with a virus and I would like to assess the depth of coverage produced by sequencing their genomes from two different sources (genomes are the same, the sources are different). Even though both sources are quite different the first step after RNA extraction is a OneStep RT-PCR. I mentione this because as you may guest already I usually get a pretty good coverage. The question here is wether those coverages are comparable.
I have 30 samples that were ran in different runs in a Mi-Seq platform. Let's say that half of the samples come from one source and that the other half from the other one. Since I want to compare them what I would like to do is to normalize the dataset. What I have in mind is to normalize by log2 instead of normalizing by total number of reads. Then calculate the Depth of coverage based on the number of reads normalized. Does it make sense? Should I go for DESeq or some other package? I think that at the end I will end up comparing the results using different approaches but I just would like some comments and suggestions.
Thanks once more.
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