Commit 9ee746cf authored by Blaise Li's avatar Blaise Li
Browse files

Trying less stringent gene selection for metagenes

Also updated gene list names.
parent d5d6959f
......@@ -169,7 +169,7 @@ ID_LISTS = [
"germline_specific",
"histone",
"spermatogenic_Ortiz_2014", "oogenic_Ortiz_2014",
"piRNA_dependent_prot_si_down4_WR_RT_top200", "piRNA_dependent_prot_si_22G_down4",
"piRNA_dependent_prot_si_22G_down4_top200", "piRNA_dependent_prot_si_22G_down4",
"csr1_prot_si_supertargets_common"]
annot_dir = config["annot_dir"]
gene_lists_dir = "/pasteur/entites/Mhe/bli/Gene_lists"
......@@ -197,9 +197,11 @@ NORM_TYPES = ["protein_coding", "median_ratio_to_pseudo_ref"]
assert set(NORM_TYPES).issubset(set(SIZE_FACTORS))
# For metagene analyses
META_MARGIN = 300
#META_MARGIN = 300
META_MARGIN = 0
META_SCALE = 2000
UNSCALED_INSIDE = 500
#UNSCALED_INSIDE = 500
UNSCALED_INSIDE = 0
#META_MIN_LEN = 1000
META_MIN_LEN = 2 * UNSCALED_INSIDE
MIN_DIST = 2 * META_MARGIN
......@@ -332,10 +334,11 @@ rule all:
trimmer=TRIMMERS, norm_type=NORM_TYPES, orientation=["all"]),
#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
expand(OPJ(
output_dir, "{trimmer}", "figures", aligner, "{lib}_by_{norm_type}_mean",
"{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)),
trimmer=TRIMMERS, lib=LIBS, norm_type=NORM_TYPES, orientation=["all"],
trimmer=TRIMMERS, lib=LIBS, norm_type=NORM_TYPES, orientation=["all", "fwd", "rev"],
biotype=METAGENE_BIOTYPES),
......@@ -1654,6 +1657,7 @@ def meta_params(wildcards):
raise NotImplementedError("Metagene analyses for %s not implemented." % biotype)
# TODO: make scripts to generate bed given gene names and one to plot the metaprofile
rule plot_meta_profile_mean:
input:
bigwig = rules.merge_bigwig_reps.output.bw,
......
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