Truncation of chimeric reads

Valid Hi-C read pairs originate from chimeric fragments with DNA from two different loci linked by the ligation junction. Diachromatic searches read sequences in 5’-3’ direction and truncates chimeric reads at the location of the ligation site, thereby removing the following sequence.

For Capture Hi-C, the sticky ends are filled in with biotinylated nucleotides, and the resulting blunt ends are ligated. The corresponding ligation junctions can then be observed as two consecutive copies of the overhang sequence at restriction enzyme cutting sites. For Capture-C, no fill in of the overhangs is performed, and the ligation junctions occur as plain restriction sites.

Use the --sticky-ends option if no fill in was performed.

Running the truncate subcommand

Use the following command to run the truncation step:

$ java -jar Diachromatic.jar truncate \
    -q test_1.fastq \
    -r test_2.fastq \
    -e HinDIII \
    -x prefix \
    -o outdir

Available arguments:

Short option	Long option	Example	Required	Description	Default
-q	--fastq-r1	forward.fq.gz	yes	Path to the forward FASTQ file.	–
-r	--fastq-r2	reverse.fq.gz	yes	Path to the reverse FASTQ file.	–
-e	--enzyme	HindIII	yes	Symbol of the restriction enzyme.	null
-s	--sticky-ends	false	no	True, if no fill-in of sticky ends was performed.	false
-o	--out-directory	cd4v2	yes	Directory containing the output of the truncate command.	results
-x	--out-prefix	stim_rep1	yes	Prefix for all generated files in output directory.	prefix

Output files

The default names of the truncated and gzipped FASTQ files are:

• prefix.truncated_R1.fastq.gz
• prefix.truncated_R2.fastq.gz

In addition, a file is produced that contains summary statistics about the truncation step.

• prefix.truncation.stats.txt