Text Outputs
Tombo provides two text outputs:
1.Genome Broser Files - Genome browser compatible per-genomic-base statistics
2.Fasta - Genomic sequence output surrounding identified modified base sites
tombo text_output browser_files
tombo text_output browser_files命令接收a set of reads（--fast5 basedirs）和/或由tombo detect_modifications命令（--statistics filename）生成的统计文件。还可以提供 set of reads（--control-fast5-basedirs）。输出文件将以variableStep-wiggle格式（或--file-type-coverage的bedgraph格式）为每个请求的统计数据（both plus and minus strands）生成。
有几个统计数据可用于output：
1.coverage-映射和validly re-squiggled reads的覆盖率水平
2.valid_coverage—mapped, validly re-squiggled且超出由--statistics-filename中指定的--single read threshold指定的间隔的的coverage level。
3.dampened_fraction-significantly modified reads的估计分数（on-level_sample_compare modified base detection methods only)）
4.fraction-significantly modified reads的 raw fraction（non-level_sample_compare modified base detection methods only)
5.statistic-从level_sample_compare方法生成的统计信息（默认输出效果大小统计信息；如果指定--store-p-value来 detect_modfications 命令，则输出负的log p-value）。
6.signal-映射到此位置的所有reads的平均信号水平
7.signal_sd—映射到此位置的所有reads的平均信号标准偏差（除非tombo resquiggle命令中提供了--include event stdev，否则不可用）
8.dwell-分配给该位置的观察到的raw observations的平均数量
9.difference-样本和control set of reads之间的标准化信号水平差异
提示：
暗示
The dampened_fraction output 将psuedo-counts添加到每个测试位置检测到的un-modified和modified reads 中（由--coverage-dampen-counts option指定），而fraction option从detect_modifications结果返回任何reference site的modified reads原始分数。dampen_fraction output旨在允许在下游分析中包含low coverage regions，而不会在top of rank lists造成潜在的false positive site。使用包含的scripts/test_beta_priors.R script可视化--coverage damp counts选项的不同值。
Motif Filtering Output
The tombo text_output browser_files contains options --motif-descriptions and --genome-fasta enabling computed statistics output to be restrcited to only those locations at known/putative motif-centered modifications. These options apply to the fraction, dampened_fraction and valid_coverage file types.
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Files will be output to individual wiggle files (two per statistic for plus and minus genomic strand) in the following format [wiggle-basename].[wiggle-type].[sample|control]?.[plus|minus].wig
tombo text_output signif_sequence_context
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tombo detect_modifications de_novo --fast5-basedirs <fast5s-base-directory> \
--statistics-file-basename sample.de_novo
tombo text_output signif_sequence_context --statistics-filename sample.de_novo.tombo.stats \
--genome-fasta reference.fasta --num-regions 1000 --num-bases 50
./meme -oc tombo.de_novo_motif_detection.meme -dna -mod zoops tombo_results.significant_regions.fasta
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