A novel bioinformatics pipeline named OCRDetector for detecting OCRs of the whole-genome based on cfDNA.
The original name is OCRDetector
email- [email protected]
Usage:
python OCRDetectBycfDNA.py [-h usage] [-i input file] [-o OCRs output bed]
Options:
-h: usage
-i: bam file list of cfDNA
-o: output file of detected OCRs
Example:
-
python OCRDetectBycfDNA.py -i bamFileList.txt -o OCRs.bed
orpython OCRDetectBycfDNA.py -i bamFileList.txt -o OCRs.bed -c -1
The above command can calculate the OCRs of the whole genome
-
python OCRDetectBycfDNA.py -i bamFileList.txt -o OCRs.bed -c 1
The above command can calculate the OCRs of chromosome 1
-
python OCRDetectBycfDNA.py -h
View the usage of the software
Guidance:
Step1:
First, you need to modify the content of the bamFileList.txt file and replace it with the path of your cfDNA-seq data. The input cfDNA-seq data file is of bam type and has been indexed.
Step2:
python OCRDetectBycfDNA.py -i bamFileList.txt -o OCRs.bed
The above command can get the initial OCRs.
Step3:
Extract features and train machine learning models to filter false positives.
Step4:
Use bedtools to calculate the intersection of our OCRs and OCRs obtained from other data (ATAC-seq, Dnase-seq, TSS of Genes ).
Waiting for subsequent updates