Input table of differential expression analysis in R

Question

[Karla T.]

Hi, everyone!

I have to analyze the result of an RNAseq with R. The experiment consisted in growing bacteria in five different culture conditions and then the total RNA of each condition was sequenced. The result they gave me was a table, which looks like this:

Gene ID         Reads Condition 1     Reads condition 2    ....(RC3,RC4).. Reads condition 5
GEN_R5                 21                    56               .........          44
GEN_R10               182                   408               .........         304
GEN_R15                3                     1                .........          7
.   
.
(3400 genes)

I have found many tutorials to process and analyze this data, but they start from sequence or alignment and I don't understand them very well.. Please, if someone can guide me from the information I have in this table or if you have any tutorial that I can follow, I would greatly appreciate it.

Thanks!

Answer 1

[h.mon]

See DESeq2 vignette, start from Count Matrix Input.

[Karla T.]

thank you thank you thank you!! :D

Answer 2

[WouterDeCoster]

A good starting point is the Bioconductor RNA-seq workflow: gene-level exploratory analysis and differential expression

but they start from sequence or alignment and I don't understand them very well..

Just because you start from read counts doesn't mean you don't have to understand the sequence and alignment part. These are vital concepts which are essential for further interpretation of your data. So even if you don't have to do those steps you still have to make sure you understand what's going on.

[Karla T.]

It is true. It's just that my brain already hurts. I was calculating everything by TPM but my advisor thought it would be "interesting" that I learned R, since nobody else knows how to use the program in the lab ...

well, thanks for your help!! :D

[WouterDeCoster]

but my advisor thought it would be "interesting" that I learned R

Honestly, it's going to be a painful trip, but everything you learn and every hour you spend learning will pay off in the long run. Not today, not this month, maybe not this year. But learning to code is a very valuable skill. Good luck.