DJ Counter

Count the number of distal junctions (DJ) of the ribosomal DNA (rDNA)

Purpose

This repository provides tools for estimating the copy number of the DJs in a genome from sequencing reads.

Principle

Copy number of DJs are determined by 1) the sequencing coverage in mapped reads or 2) k-mer multiplicity in raw reads.

Main workflow

Copy number of the DJ can be estimated with the following approaches:

1. Mapping based approach
2. K-mer based, reference-free approach

Mapping based estimates

The mapping based approach is recommended when the reads are already aligned to one of the following references.

1. GRCh38/hg38 Homo_sapiens_assembly38.fasta.gz (1000 Genomes Project Broad ver. Suitable for UKBioBank) or GRCh38_full_analysis_set_plus_decoy_hla.fa (1000 Genomes Project NYGC ver. Suitable for 1KGP NYGC 30x cram)

   Requires chr21, chr17_GL000205v2_random and chrUn_GL000195v1.

2. GRCh37/hg19 human_g1k_v37.fasta.gz (1000 Genomes Project ver)

   Requires chr7_gl000195_random and chr17_gl000205_random.

3. T2T-CHM13/hs1 (Will be updated soon)

For hg38 or hg19, check with samtools to confirm the sequence exists in the header; such as using samtools view -H in.bam | grep chr17_GL000205v2_random.

Read coverage is assessed on the mapped BAM file for the target DJ region and compared against the background coverage collected from autosomes.

K-mer based approach

The k-mer based approach is reference-free.

This approach is recommended when reads are aligned to hg38 or hg19 without any decoy sequences or are in its raw FASTQ form. A collected set of target k-mers are pre-built to query the k-mer multiplicity of the DJ and is compared against the single / 2-copy copy number estimates inferred from the k-mer multiplicity histogram.

Change logs

v0.1(2024-07-17)

* first commit

v0.2(2024-07-25)

* Changing the background coverage estimation methods from samtools idxstats to samtools coverage.
* Removing the step of saving temporary files; instead, we assign everything to variables.

v0.2.1(2024-07-29)

* Add background and fragment size to the output file.
* Fix the command line used for calculating the background to ensure it works correctly.

v0.2.2(2025-11-26)

* Add BED file for roi on hg19