TOuCAN Results

This Page explains all the results for the T2C and the HiC analysis coming from TOuCAN.

T2C Results: File System

TOuCAN sorts the output of the T2C analysis in different directories. Inside the given output directory, it generates the following structure:

/OUT/
	./restriction_maps/
	./bam/
	./stats/
	./Interactions/
		./01_all_interactions_bed_raw/
		./02_all_interactions_bed_norm/
		./03_target_region_interactions_bed/
		./04_final_interactions_annotated/
		./05_interactions_viewpoint_annotated/
	./plots/
		./interaction_plot/
		./multiplot/
		./TAD/
	./TAD/
	[./fastq/]
	[./additional_files/]
		./IFMatrix/
		./sai/
		./sam/
		./bai/
		./bam/
		./bed/
	[./uropa/]

restiction_maps

This directory will be created if no restriction maps are given for the analysis. TOuCAN generates the restriction maps and saves those inside this directory. For the next run with those restriction maps, you can set this directory as parameter inside the configuration file.

bam

All generated bam files are stored in this directory. If you want to run the analysis again with the same sample, you can skip the alignment step by giving the bam file as a command line parameter.

stats

The flagstats and further statistics are stored in this directory. For example the average count of read-pairs per interaction.

Interactions

Stores all text-based files containing the information about all found interactions.

01_all_interactions_bed_raw

Contains the interaction bed files without normalization. The file is tab delimited. It contains all found interactions on the whole genome.
Columns: chr1 start1 end1 chr2 start2 end2 score_raw

02_all_interactions_bed_norm

Contains the interaction bed files with normalization. The file is tab delimited. It contains all found interactions on the whole genome.
Columns: chr1 start1 end1 chr2 start2 end2 score

03_target_region_interactions_bed

Contains the interaction bed files with normalization. The file is tab delimited. It contains only the interactions inside the given target region.
Columns: chr1 start1 end1 chr2 start2 end2 score

04_final_interactions_annotated

Contains the final interaction bed files with normalization. The file is tab delimited. It contains only the interactions inside the given target region. Every Fragment is annotated with uropa. If uropa could not find an annotation the value shown is 'NA'.
Columns: chr1 start1 end1 chr2 start2 end2 score uropa_annotation_for_fragment_1 uropa_annotation_for_fragment_2

For more insight, read the uropa documentation.

05_interactions_viewpoint_annotated

Contains the viewpoint files. Viewpoint files contain the same information as the final interaction files but with a different easy to read format.
Each fragment (chr start end uropa_annotation) builds a header. Under each header are all fragments listed which interact with the header fragment. Those fragments are tab-indented. The listed fragments contain an additional column with the normalized interaction score.

For example:

chr4	137286307	137293624	CDS	137289114	137289349	+	end	617	FeatureInsidePeak	0.04	1	ENSMUSG00000036856	Wnt4	protein_coding	2	1	protein_coding	0
	chr4	137293631	137306208	95.0388141711657	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0
	chr4	137321752	137324423	0.798645497236687	CDS	137322533	137322619	-	start	469	FeatureInsidePeak	0.04	1	ENSMUSG00000006699	Cdc42	protein_coding	2	2	protein_coding	0
	chr4	137430270	137431969	0.798645497236687	CDS	137430460	137430499	-	start	621	FeatureInsidePeak	0.03	1	ENSMUSG00000023433	Cela3b	protein_coding	2	1	protein_coding	0
	chr4	137546309	137548691	0.798645497236687	CDS	137548021	137548172	+	start	521	FeatureInsidePeak	0.07	1	ENSMUSG00000028763	Hspg2	protein_coding	3	5	protein_coding	0
	chr4	137604301	137606064	0.798645497236687	CDS	137604523	137604643	+	end	539	FeatureInsidePeak	0.07	1	ENSMUSG00000043411	Usp48	protein_coding	2	1	protein_coding	0
	chr4	137822263	137824140	1.59729099447337	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0

plots

Stores all plots generated by TOuCAN.

interaction_plot

The interaction plot is the main plot of the T2C analysis. It shows a typical T2C (pyramid) plot.
For more information about T2C and its plot, read the original paper.

multiplot

The MultiPlot combines the interaction plot with a TAD boundary plot and gene annotation. For more information about the TAD boundaries and the tool RobusTAD which TOuCAN uses, follow this link.

TAD

Contains the single TAD boundary plot as PDF.

TAD

Contains the files generated by RobusTAD which are used for the TAD boundary score plot.

fastq [only if safe_all_files is set to 1]

Contains the decompressed fastq files.

additional_files [only if safe_all_files is set to 1]

Contains a variety of files generated by the analyzing steps. [comming soon]

uropa [only if safe_all_files is set to 1]

Contains all files generated by uropa.