Entering edit mode
6.5 years ago
Fatima
▴
1000
Hello everyone,
I have mapped a few reads to several reference genomes and have measured gene expression (expression level of a bunch of genes in these genomes). The expression level I measured is simply coverage/length of gene. I need to analyze the data, I was looking for some insights on which tests to do, or which plots to draw to get a sense of how to interpret these results. For example somewhere I read log transformation of expression levels is a better measure. Is there any test I can do? T-test or something like that. I'm a newbie and have no idea what to use.
Have a look at this workflow: https://www.bioconductor.org/help/workflows/rnaseqGene/
"I have mapped a few reads to several reference genomes" - why? The only reference genome that is relevant is the genome of the species the data came from.
In metagenomics, we use a mixture of species as reference genome :)
Details like that are really important - why was this not in your original question?
I didn't know it's confusing. I have only worked with metagenomics and metatranscriptomics datasets, so I didn't realize that what I'm doing is different from regular gene expression.
That's indeed often the problem - but don't hesitate to add such information when asking questions. Better to be a bit redundant than to miss important parts. I'm completely useless when it comes to metagenomics, and the workflow I suggested may not be the most appropriate for this experiment.
Please update your question with all relevant information (species, number of samples, the aim of your analysis,...). Updating your first post will bump your question back to the top (just don't abuse this feature...).