Commit 79f9780b authored by Blaise Li's avatar Blaise Li
Browse files

Output RPM folds for all_si_22G.

This is an attempt to generate more interesting output when the genome
has extra transgenes.
parent 7a5d7c85
......@@ -849,6 +849,8 @@ rule all:
#expand(OPJ(feature_counts_dir, "summaries", "{lib}_{rep}_nb_non_structural.txt"), filtered_product, lib=LIBS, rep=REPS),
#OPJ(mapping_dir, f"RPM_folds_{size_selected}", "all", "pisimi_mean_log2_RPM_fold.txt"),
OPJ(mapping_dir, f"RPM_folds_{size_selected}", "all", f"pimi{SI_MIN}G_mean_log2_RPM_fold.txt"),
# To have RPM (folds) for transgenes (which are not in prot_si category)
OPJ(mapping_dir, f"RPM_folds_{size_selected}", "all", f"all_si_{SI_MIN}G_mean_log2_RPM_fold.txt"),
# Not looking ad deseq2 results any more
#expand(OPJ(mapping_dir, f"deseq2_{size_selected}", "all", "pisimi_{fold_type}.txt"), fold_type=["log2FoldChange"]),
#expand(OPJ(mapping_dir, "RPM_folds_%s" % size_selected, "{contrast}", "{contrast}_{small_type}_RPM_folds.txt"), contrast=IP_CONTRASTS, small_type=DE_TYPES),
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