Entering edit mode
19 months ago
Mir-Mammad
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0
I would like to perform a differential expression analysis of the coag sample we produced in the lab. I have performed RNA-seq analysis before, but this one looks tricky. Overall, I have 3 samples alone bacteria X and Y, and XY together. My goal is to evaluate how many reads map to both species, and I am struggling to come up with solutions for this problem. Are there any resources on how to perform this type of analysis?
Do you have the reference genomes? Also, do you have any biological replicates of X, Y and XY?
yes, X is Actinomyces naeslundii str. Howell 279 and Y is Corynebacterium matruchotii ATCC 14266. both of them are on Ensembl website so I was able to build reference for each of those individually
So if you'll build a reference of both together you should be able to map the reads to each genome. You'll have to look out for multi mapping reads as those might interfere with your read count but as long as you map all samples against the same reference it shouldn't be an issue.
How different are the bacteria? If there's < 90% similarity you should be able to map RNA to a specific genome.