Compute TPM and "efficiencies" on protein_coding.

Degradome-seq/Degradome-seq.snakefile

@@ -130,7 +130,7 @@ rule all:
         #     lib=LIBS, biotype=["alltypes"], orientation=ORIENTATIONS),
         expand(
             OPJ(counts_dir, "diff_%s" % eff_name, "{contrast}", "{orientation}_{biotype}", "{contrast}_diff_%s.txt" % eff_name),
-            contrast=DD_CONTRASTS, orientation=["fwd"], biotype=["alltypes"]),
+            contrast=DD_CONTRASTS, orientation=["fwd"], biotype=["alltypes", "protein_coding"]),
 
 
 include: ensure_relative(irules["link_raw_data"], workflow.basedir)

PRO-seq/PRO-seq.snakefile

@@ -357,7 +357,7 @@ rule all:
         expand(OPJ(
             "{trimmer}", aligner, "mapped_C_elegans", "{counter}",
             "all_on_C_elegans", "{biotype}_{orientation}_TPM.txt"),
-            trimmer=TRIMMERS, counter=COUNTERS, biotype=["alltypes"], orientation=ORIENTATIONS),
+            trimmer=TRIMMERS, counter=COUNTERS, biotype=["alltypes", "protein_coding"], orientation=ORIENTATIONS),
         #expand(OPJ("{trimmer}", "figures", aligner, "{lib}_mean", "{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)), trimmer=TRIMMERS, lib=LIBS, orientation=["all"], biotype=["protein_coding"]),
         #expand(OPJ("{trimmer}", "figures", aligner, "{lib}_mean", "{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)), trimmer=TRIMMERS, lib=LIBS, orientation=["all"], biotype=METAGENE_BIOTYPES),
         # TODO: Add metagene profiles similar to small RNA-seq

RNA_Seq_Cecere/RNA-seq.snakefile

@@ -318,7 +318,7 @@ counts_files = [
         OPJ(aligner, f"mapped_{genome}", "{counter}",
             "all_{mapped_type}", "{biotype}_{orientation}_TPM.txt"),
         counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
-        biotype=["alltypes"], orientation=ORIENTATIONS),
+        biotype=["alltypes", "protein_coding"], orientation=ORIENTATIONS),
     expand(
         OPJ(aligner, f"mapped_{genome}", "{counter}",
             "all_{mapped_type}", "{biotype}_{orientation}_RPK.txt"),

Ribo-seq/Ribo-seq.snakefile

@@ -579,7 +579,7 @@ rule all:
         # translation_efficiency
         expand(
             OPJ(counts_dir, "{lib}_mean_{read_type}_on_%s" % genome, "{lib}_{biotype}_{orientation}_%s.txt" % eff_name),
-            lib=EFF_LIBS, read_type=["RPF"], biotype=["alltypes"], orientation=["fwd"]),
+            lib=EFF_LIBS, read_type=["RPF"], biotype=["alltypes", "protein_coding"], orientation=["fwd"]),
         # DESeq2 results
         expand(
             OPJ(
@@ -599,7 +599,7 @@ rule all:
                 counts_dir,
                 "diff_%s_{read_type}" % eff_name,
                 "{contrast}", "{orientation}_{biotype}", "{contrast}_diff_%s.txt" % eff_name),
-            read_type=["RPF"], contrast=DT_CONTRASTS, orientation=["fwd"], biotype=["alltypes"]),
+            read_type=["RPF"], contrast=DT_CONTRASTS, orientation=["fwd"], biotype=["alltypes", "protein_coding"]),
 
 # rule future_all:
 #         meta_profiles,