I am having prblems with the sample sheet and contrast sheet (the problem is with the condition column, because I don´t know if it has to mach with the header of the contrast sheet, or with the parameters specified in the contrast sheet). • Please note that in the sample sheet there are samples with a "control" condition that are not shown in the screenshot. I'm attaching two screenshots because I don't know if I'm doing it the right way (first: contrast sheet, second: sample sheet). Thank you!

The

condition

column in the sample sheet has to match the body of the contrast sheet, e.g.

TREATMENT

. Sometimes you may just have two condition and there is a single non-header line in the contrast sheet, like your example, but you could have several contrasts (e.g. several treatments against the same control, or other combinations), so using the header would not work in these cases.

But in this case, the pipeline doesn´t complain about the missmatch and I get a table of counts. Does it make sense? Thank you!

I don't know if this is case-sensitive, maybe

treatment

is the same as

TREATMENT

to the pipeline ...

It is better as you told me in order to avoid errors, I have checked it.