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TOuCAN Results
This Page explains all the results for the T2C and the HiC analysis coming from TOuCAN.
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/]
This directory will be created if no restriction maps are given for the analysis. TOuCAN generates the restriction maps and safes those inside this directory. For the next run with those restriction maps you can set this directory as parameter inside the configuration file.
In this directory all the generated bam files are stored. If you want to run the analysis again with the same sample you can skip the alignment step with giving the bam file as a command line parameter.
In this directory the flagstats and further statistics are stored. for example the average count of read-pairs per interaction.
Stores all text based files containing the information about all found interactions.
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
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
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
Contains the final interaction bed files with normalization. The file is tab delimited. It It contains only the interactions inside the given target region. Every Fragment is annotated with uropa. If uropa could not find a 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.
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 a 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
Stores all plots generated by TOuCAN.
The interaction plot is the main plot from the T2C analysis. It shows a typical T2C (pyramid) plot.
For more information about T2C and its plot read the original paper.
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
Contains the single TAD boundary plot as PDF.
Contains the files generated by RobusTAD, which are used for the TAD boundary score plot.
Contains the decompressed fastq files.
Contains a variety of files generated by the analysing steps. [comming soon]
Contains all files generated by uropa.