Understanding RNA-seq data

Question

[newacclol]

Hi, Biostars. I have a question.

I am a beginner in bioinformatics and I am struggling to understand the data I am supposed to work with. I googled it up and got back to the original article that introduced this dataset, but it looks like my knowledge was not sufficient to understand the information I found. I have a set of RNAseq data which looks like this:

Gene ID phase1  phase2  phase3  phase4  phase5  phase6  phase7  sum
gene1   32.22   4.01    3.8     1.62    4.83    1.07    1.15    48.7
gene2   5.97    0.77    2.14    0       2.83    1.9     2.99    16.6
gene3   2.13    0.15    0.06    0.16    0.09    0.05    0       2.64
gene4   4.56    4.79    15.88   1.11    5.66    2.25    2.66    36.91
gene5   1.52    0       2.23    0       9.43    3.75    0       16.93

It's gene IDs and gene expression for a particular life stage of that organism. The question is: What do the numbers mean? What does it mean that, for example, for gene 1 the expression in life phase 1 is 32.22, and in life phase 2 it's 4.01?

Answer 1

[swbarnes2]

No one can tell you from that. It's probably not counts, since the numbers are not integers (But RSEM can return expected counts that are not integers). It might be counts corrected for transcript length and total # of reads, or counts corrected for the total # of reads only.

[newacclol]

Thank you for your reply, @swbarnes2. This data was not obtained from one individual, so could it be that it's just average values of something?

Given it would be the counts, counts of what do you mean? (I am sorry for asking such basic questions).

[matthew.higgins2017]

Hi newacclol, The counts refer to the number of reads which map to that particular gene locus. If you are new to RNA-seq a great tutorial which I completed when I first started can be found at: https://github.com/griffithlab/rnaseq_tutorial/wiki

[newacclol]

Thank you, @matthew.higgins2017. :) I will check it out this weekend.