inst/script/description_of_extdata.md

In hw538/cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

A description of example files in this package.

txt files in inst/extdata/groups_picard

This folder contains txt files from four cohorts. i.e. cohort_1, _2, _3 and _4. All of the txt files were artificial files(thus the data inside) generated manually, it mimics the output of the collectInsertSize function in PICARD tools, detailed usage of this tool please see: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics

As mentioned in the cfDNAPro user manual, these txt files are the output of 'collectInsertSize` function in PICARD tools using bam files as its input. Users could get these txt files using their own bam files, and the bam files could be generated after alignment of Illumina NGS sequencing data.

txt files in inst/extdata/step6/example

All of the txt files were artificial files(thus the data inside) generated manually, it mimics the output of the collectInsertSize function in PICARD tools, detailed usage of this tool please see: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics

As mentioned in the cfDNAPro user manual, these txt files are the output of 'collectInsertSize` function in PICARD tools using bam files as its input. Users could get these txt files using their own bam files, and the bam files could be generated after alignment of Illumina NGS sequencing data.

hw538/cfDNAPro documentation built on Jan. 15, 2025, 12:20 a.m.