References¶
Options¶
옵션 테이블 입니다.
| Option | Parameter/default | Description |
|---|---|---|
| Required arguments | ||
| --bam_path | {.bam folder path} | Specify .bam files folder |
| --sample_path | {file} | Specify sample list file |
| --normal_path | {.bam folder path} | Specify .bam files folder of normal sample |
| --refseq_path | {file} | Specify refseq file of tsv |
| --variants_path | {file} | Specify generic variants file of tsv |
| --refseq | {NMID} | Specify nmid to draw |
| --prefix | {file without extension} | Specify output file path |
| Optional arguments | ||
| Drawing graph | ||
| --output_prefix | {file without extension} | Specify output file path |
| --combine_slices | Combine all sliced graphs | |
| --cureated_genes | {file} | Specify curated genes tsv file |
| --draw_average_line | Draw average line of all coverages | |
| --draw_span | {10000} | Specify span of each slice (bp) |
| --exclude_exon | {num1,num2,…} | Specify exons excluded |
| --exon_sliced | Slice the graph by exon of selected gene | |
| --exon_space | {0} | Specify margin of slice by exons |
| --font_size | {7} | Specify font size of whole graph |
| --marker_size | {9} | Specify marker size of generic variants |
| --min_max | Draw min/max graph and fill between two graphs | |
| --ylim | {10} | Set y limit of graph |
| Smoothing | ||
| --smoothing | {average}, {loess} | Specify smoothing option |
| --average | {0} | Set bp of average smoothing |
| --fill | Smooth graph with interval of --average |
|
| Clustering | ||
| --clustering | Clustering sample into two groups | |
| --clustering_mode | {silhouette}, {nmf}, {splice_site} | Specify clustering mode |
| --select_exon | {num1,num2} | Select two exon to cluster samples |
| --score_plot_width | {12} | Set width of ci/tau/score plot |
| --score_plot_height | {12} | Set height of ci/tau/score plot |
| --limit_tau | {int} | Set high limit of silhouette clustering |
| --limit_tau_low | {int} | Set low limit of silhouette clustering |
| --silhouette_dintv | {30} | Set space of clustering from two exons border |
Outputs¶
출력 테이블 입니다.
| Filename | Main associated command(s) | Description |
|---|---|---|
<prefix>.pdf |
--output_prefix | Draw graph of coverage of all samples (combined) |
<prefix> _{num}.pdf |
--output_prefix | Draw graph of coverage of all samples (sliced) |
<prefix> _silhouette_plot.pdf |
--clustering_mode | Draw ci/tau/score graph |
<prefix> _ratio_score_plot.pdf |
--clustering_mode | Draw ratio/score graph |