if you use something different than treatment vs control, the pipeline will fail in the anota2seqrun R script because the order of contrast and the levels of sample_treatment_col doesn't need to be the same, since they are sorted by alphanumeric characters.
One line in that script to relevel that column with the contrast reference information will fix it
Description of the bug
if you use something different than treatment vs control, the pipeline will fail in the anota2seqrun R script because the order of contrast and the levels of sample_treatment_col doesn't need to be the same, since they are sorted by alphanumeric characters.
One line in that script to relevel that column with the contrast reference information will fix it
Command used and terminal output
No response
Relevant files
No response
System information
No response