Commit a060de10 authored by Blaise Li's avatar Blaise Li
Browse files

Ask for TPM output for GRO-seq pipeline.

parent c8394f0a
......@@ -153,7 +153,7 @@ RMSK_FAMILIES_BIOTYPES = [
BIOTYPES_TO_JOIN = {
"all_rmsk": [biotype for biotype in COUNT_BIOTYPES if biotype in RMSK_BIOTYPES],
"all_rmsk_families": [biotype for biotype in COUNT_BIOTYPES if biotype in RMSK_FAMILIES_BIOTYPES],
# We only count "protein_coding", not "protein_codin_{5UTR,CDS,3UTR}"
# We only count "protein_coding", not "protein_coding_{5UTR,CDS,3UTR}"
"alltypes": [biotype for biotype in COUNT_BIOTYPES if not biotype.startswith("protein_coding_")]}
JOINED_BIOTYPES = list(BIOTYPES_TO_JOIN.keys())
DE_BIOTYPES = [biotype for biotype in LFC_RANGE.keys() if biotype in COUNT_BIOTYPES + JOINED_BIOTYPES]
......@@ -332,6 +332,10 @@ rule all:
output_dir, "{{trimmer}}", aligner, "mapped_C_elegans",
"{lib}_{rep}_on_C_elegans_by_{{norm_type}}_{{orientation}}.bw"), filtered_product, lib=LIBS, rep=REPS),
trimmer=TRIMMERS, norm_type=NORM_TYPES, orientation=["all"]),
expand(OPJ(
output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{counter}",
"all_on_C_elegans", "{biotype}_{orientation}_TPM.txt"),
trimmer=TRIMMERS, counter=COUNTERS, biotype=["alltypes"], orientation=ORIENTATIONS),
#expand(OPJ(output_dir, "{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(output_dir, "{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
......
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