diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index cad4927a7a694765bd394dee1eeaa65c57182f39..a397d52ee82a80dfb7b83ab4e08346a004f32889 100644 --- a/small_RNA-seq/small_RNA-seq.snakefile +++ b/small_RNA-seq/small_RNA-seq.snakefile @@ -515,9 +515,10 @@ TESTED_SIZE_FACTORS = ["mapped", "non_structural", "all_sisiuRNA", "piRNA", "miR # and then substraction of a pseudocount, in order to deal with zero counts. # This seems to perform well (see "test_size_factor" results). DE_SIZE_FACTORS = ["non_structural", "median_ratio_to_pseudo_ref"] -SIZE_FACTORS = ["non_structural", "piRNA"] +SIZE_FACTORS = config.get("size_factors", ["non_structural"]) #NORMALIZER = "median_ratio_to_pseudo_ref" -RPM_NORMS = config.get("rpm_norms", SIZE_FACTORS) +# Do we really need distinct lists of normalizers? +RPM_NORMS = SIZE_FACTORS RPM_FOLD_TYPES = [ f"mean_log2_RPM_by_{norm}_fold" for norm in RPM_NORMS]