qualimap.md

The installation and usage of Qualimap

1. About

Bam file QC.

2. Installation

mamba install -c bioconda qualimap

3. Usage

qualimap bamqc -bam /home/qgn1237/qgn1237/4_single_cell_SV_chimera/20230624_1st_PC3_bulk_ONT_DNA_MK1c/data_QC_assessment_comparison/PC3_Pacbio_hifi_DNA/PC3_hifi_DNA_3X_downsampled/PC3_3X.bam -c -outdir /home/qgn1237/qgn1237/4_single_cell_SV_chimera/20230624_1st_PC3_bulk_ONT_DNA_MK1c/data_QC_assessment_comparison/PC3_Pacbio_hifi_DNA/PC3_hifi_DNA_3X_downsampled/qualimap --java-mem-size=70G