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postprocess.yaml
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{% set organism_db="/usr/users/ssohrab/CLIP" %}
{% set gff_db = organism_db + "/Annotations" %}
{% set genome_file = organism_db + "/Reference_genome/WholeGenomeFasta/genome.fa" %}
{% set filter_gff = gff_db + "/R64-2-1_genes.gff" %}
{% set negative_set_gff = gff_db + "/R64-2-1_genes.gff" %}
{% set tRNA_gff = gff_db + "/R64-2-1_tRNA_gene.gff" %}
{% set rRNA_gff = gff_db + "/R64-2-1_rRNA_gene.gff" %}
{% set snRNA_gff = gff_db + "/R64-2-1_snRNA_gene.gff" %}
{% set snoRNA_gff = gff_db + "/R64-2-1_snoRNA_gene.gff" %}
{% set intron_gff = gff_db + "/R64-2-1_introns.gff" %}
{% set bootstrap_iter = 2500 %}
{% set n_processes = 6 %}
{% set skip_cp = False %}
{% set skip_hm = False %}
{% set skip_xx = False %}
{% set skip_km = False %}
pipeline:
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: tRNA-plot CenterPlot
gff_file: {{ tRNA_gff }}
output_prefix: tRNA_gene
downstream_bp: 100
upstream_bp: 100
gene_bp: 30
min_trscr_size_bp: 50
max_trscr_size_bp: 250
smoothing_window: 5
labelCenterA: 5' end
labelCenterB: 3' end
labelBody: tRNA body
remove_tmp_files: yes
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- CenterPlotBSModule:
skip: no
skip: {{ skip_cp }}
module_info: rRNA-plot CenterPlot
gff_file: {{ rRNA_gff }}
output_prefix: rRNA_gene
downstream_bp: 100
upstream_bp: 100
gene_bp: 50
min_trscr_size_bp: 100
max_trscr_size_bp: 5000
smoothing_window: 5
labelCenterA: 5' end
labelCenterB: 3' end
labelBody: rRNA body
remove_tmp_files: yes
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- GffFilterModule:
filter_gff: {{ filter_gff }}
padding_bp: 10
features:
- tRNA_gene
- snRNA_gene
- snoRNA_gene
- rRNA_gene
file_postfix: filtered
keep_all: yes
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: Steinmetz CenterPlot 500bp+
gff_file: {{ gff_db }}/steinmetz_transcripts_tifs_clean_sorted.gff
output_prefix: steinmetz
downstream_bp: 500
upstream_bp: 500
gene_bp: 250
min_trscr_size_bp: 500
max_trscr_size_bp: 5000
smoothing_window: 21
labelCenterA: TSS
labelCenterB: pA
labelBody: Genebody
remove_tmp_files: yes
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: Steinmetz CenterPlot 1500bp+
gff_file: {{ gff_db }}/steinmetz_transcripts_tifs_clean_sorted.gff
output_prefix: steinmetz
downstream_bp: 1000
upstream_bp: 1000
gene_bp: 750
min_trscr_size_bp: 1500
max_trscr_size_bp: 5000
smoothing_window: 41
labelCenterA: TSS
labelCenterB: pA
labelBody: Genebody
remove_tmp_files: yes
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: Non-overlapping_ORF-T CenterPlot 1500bp+
type: center_plot_bs
gff_file: {{ gff_db }}/nonoverlapping_ORF-T.gff
output_prefix: nonovl_orf_t
downstream_bp: 1000
upstream_bp: 1000
gene_bp: 750
min_trscr_size_bp: 1500
max_trscr_size_bp: 5000
smoothing_window: 41
labelCenterA: TSS
labelCenterB: pA
labelBody: Genebody
remove_tmp_files: yes
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: Intron CenterPlot 80bp-200bp
gff_file: {{ intron_gff }}
output_prefix: intron
downstream_bp: 40
upstream_bp: 40
gene_bp: 40
min_trscr_size_bp: 80
max_trscr_size_bp: 200
smoothing_window: 5
labelCenterA: Donor site
labelCenterB: Acceptor site
labelBody: Intron body
remove_tmp_files: yes
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: Intron CenterPlot 150bp+
gff_file: {{ intron_gff }}
output_prefix: intron
downstream_bp: 75
upstream_bp: 75
gene_bp: 75
min_trscr_size_bp: 150
max_trscr_size_bp: 5000
smoothing_window: 9
labelCenterA: Donor site
labelCenterB: Acceptor site
labelBody: Intron body
remove_tmp_files: yes
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- HeatmapPlotModule:
skip: {{ skip_hm }}
module_info: Steinmetz Heatmap
gff_file: {{ gff_db }}/steinmetz_transcripts_tifs_clean_sorted.gff
output_prefix: steinmetz_heatmap_plot
downstream_bp: 4000
upstream_bp: 1000
min_trscr_size_bp: 0
max_trscr_size_bp: 5000
xbins: 500
ybins: 500
x_pixels: 500
y_pixels: 500
remove_tmp_files: yes
- HeatmapSmallPlotModule:
skip: {{ skip_hm }}
module_info: Steinmetz Heatmap Small
gff_file: {{ gff_db }}/steinmetz_transcripts_tifs_clean_sorted.gff
output_prefix: steinmetz_heatmap_sm_plot
downstream_bp: 500
upstream_bp: 1000
min_trscr_size_bp: 0
max_trscr_size_bp: 5000
xbins: 500
ybins: 500
x_pixels: 500
y_pixels: 500
remove_tmp_files: yes
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: CDS 1000+
gff_file: {{ gff_db }}/salma/CDS_nonoverlapping_sense_TSS_700.gff
output_prefix: ORF_NoOv_sense_TSS
downstream_bp: 1000
upstream_bp: 1000
gene_bp: 750
min_trscr_size_bp: 1000
max_trscr_size_bp: 5000
smoothing_window: 41
labelCenterA: TSS
labelCenterB: pA
labelBody: genebody
remove_tmp_files: no
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: CDS 1000+
gff_file: {{ gff_db }}/salma/CDS_nonoverlapping_sense_pA_700.gff
output_prefix: ORF_NoOv_sense_pA
downstream_bp: 1000
upstream_bp: 1000
gene_bp: 750
min_trscr_size_bp: 1000
max_trscr_size_bp: 5000
smoothing_window: 41
labelCenterA: TSS
labelCenterB: pA
labelBody: genebody
remove_tmp_files: no
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: CDS 1000+
gff_file: {{ gff_db }}/salma/TIF_nonoverlapping_sense_TSS_700.gff
output_prefix: TIF_NoOv_sense_TSS
downstream_bp: 1000
upstream_bp: 1000
gene_bp: 750
min_trscr_size_bp: 1000
max_trscr_size_bp: 5000
smoothing_window: 41
labelCenterA: TSS
labelCenterB: pA
labelBody: genebody
remove_tmp_files: no
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}
- CenterPlotBSModule:
skip: {{ skip_cp }}
module_info: CDS 1000+
gff_file: {{ gff_db }}/salma/TIF_nonoverlapping_sense_pA_700.gff
output_prefix: TIF_NoOv_sense_pA
downstream_bp: 1000
upstream_bp: 1000
gene_bp: 750
min_trscr_size_bp: 1000
max_trscr_size_bp: 5000
smoothing_window: 41
labelCenterA: TSS
labelCenterB: pA
labelBody: genebody
remove_tmp_files: no
bootstrap_iter: {{ bootstrap_iter }}
n_processes: {{ n_processes }}