diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index db224ae69bad78b0feb351b0d1b7a9dd36e2571f..58f61707d97d0158e62e03b0171f72335954cc27 100644 --- a/small_RNA-seq/small_RNA-seq.snakefile +++ b/small_RNA-seq/small_RNA-seq.snakefile @@ -1,4 +1,4 @@ -# Copyright (C) 2020 Blaise Li +# Copyright (C) 2020-2022 Blaise Li # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -495,14 +495,14 @@ COND_COLUMNS = pd.DataFrame(CONDITIONS).assign( #SIZE_FACTORS = ["raw", "deduped", size_selected, "mapped", "siRNA", "miRNA"] #SIZE_FACTORS = [size_selected, "mapped", "miRNA"] # TESTED_SIZE_FACTORS = ["mapped", "non_structural", "siRNA", "miRNA", "median_ratio_to_pseudo_ref"] -TESTED_SIZE_FACTORS = ["mapped", "non_structural", "all_sisiuRNA", "miRNA", "median_ratio_to_pseudo_ref"] +TESTED_SIZE_FACTORS = ["mapped", "non_structural", "all_sisiuRNA", "piRNA", "miRNA", "median_ratio_to_pseudo_ref"] #SIZE_FACTORS = ["mapped", "miRNA", "median_ratio_to_pseudo_ref"] # "median_ratio_to_pseudo_ref" is a size factor adapted from # the method described in the DESeq paper, but with addition # 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"] +SIZE_FACTORS = ["non_structural", "piRNA"] #NORMALIZER = "median_ratio_to_pseudo_ref" # For metagene analyses