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Commit 84611f58 authored by Blaise Li's avatar Blaise Li
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Try to add all_siRNA to some sRNA analyses.

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small_RNA-seq/small_RNA-seq.snakefile
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...@@ -456,7 +456,7 @@ ANNOT_COUNTS_TYPES_U = [ ...@@ -456,7 +456,7 @@ ANNOT_COUNTS_TYPES_U = [
f"all_siu_{SI_MIN}G", f"all_siu_{SI_MAX}G", f"all_siu_{SI_MIN}G", f"all_siu_{SI_MAX}G",
*SIU_TYPES] *SIU_TYPES]
feature_counts_dir = OPJ(mapping_dir, "feature_count") feature_counts_dir = OPJ(mapping_dir, "feature_count")
READ_TYPES_FOR_COUNTING = [f"{size_selected}_and_nomap_siRNA", f"prot_si_{SI_MIN}GRNA_and_prot_siu_{SI_MIN}GRNA", *type2RNA([f"prot_si_{SI_MIN}G", f"prot_si_{SI_MAX}G"])] READ_TYPES_FOR_COUNTING = ["all_siRNA", f"{size_selected}_and_nomap_siRNA", f"prot_si_{SI_MIN}GRNA_and_prot_siu_{SI_MIN}GRNA", *type2RNA([f"prot_si_{SI_MIN}G", f"prot_si_{SI_MAX}G"])]
# Reads remapped and counted using featureCounts # Reads remapped and counted using featureCounts
REMAPPED_COUNTED = [ REMAPPED_COUNTED = [
f"{small_type}_{mapping_type}_{biotype}_{orientation}_transcript" for ( f"{small_type}_{mapping_type}_{biotype}_{orientation}_transcript" for (
... ...
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