Scripts to replicate the results in Ju et al. Cell Reports Methods 2024

Distributed under the CC BY-NC-ND 4.0 license for personal and academic usage only.

IMPORTANT NOTE: Unauthorized commercial usages are strictly forbidden!!!

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The following software/packages are required:

1. samtools
2. bedtools
3. ichorCNA
4. R packages: creditmodel, gbm, caret, pROC, dplyr, Rmisc, ggplot2

The following files are required (they're too large to be included in this package):

1. Hg38 human reference genome

You can download the file from

https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.fa.gz

2. GM12878 nucleosome track

You can download the file from

https://download.cncb.ac.cn/nucmap/organisms/v1/Homo_sapiens/byDataType/Nucleosome_peaks_DANPOS/Homo_sapiens.hsNuc0390101.nucleosome.DANPOSPeak.bed.gz

then use following command to parse this file:

zcat Homo_sapiens.hsNuc0390101.nucleosome.DANPOSPeak.bed.gz | \
perl -lane '$c=($F[1]+$F[2])>>1; print join("\t", $F[0], $c-73, $c+1+73, $F[3]) if $F[0]=~/chr\d+$/' | \
sort -k1,1 -k2,2n | gzip >hsNuc0390101.DANPOSPeak.ext73.bed.gz

End selection

The script is calc.cfDNA.features.with.end.selection.sh under end.selection directory. To run it, you need to prepare a 2-column file that records the sample id and path to the bed file from paired-end cfDNA sequencing reads (could be gzipped) separated by TAB. Here is an example of this file:

s1	/path/to/s1.bed.gz
s2	/path/to/s2/s2.bed.gz

For BED format, please see https://genome.ucsc.edu/FAQ/FAQformat.html#format1 (the first 6 columns are required). Here are some example records for BED file:

chr1	805429	805626	LH00128:50:222KJ3LT4:7:1389:34785:19840	31	-
chr1	805768	805955	LH00128:50:222KJ3LT4:7:2219:47967:23637	30	+
chr1	806265	806427	LH00128:50:222KJ3LT4:7:2248:21854:11324	32	+

The EXCEL model

The script to build EXCEL model is do.EXCEL.sh under EXCEL directory. We had already included the features for Cristiano et al. dataset, and this script will build 3 EXCEL models using N-index, Delta-S, and Delta-M features, respectively.