QualiMap

学习资源

• Sample data and output
• source code

BAM QC

doc

samtools  sort HG00096.chrom20.bam  -@ 10   -o HG00096.chrom20.sort.bam

qualimap bamqc -bam  HG00096.chrom20.sort.bam -c -nw 400 -hm 3

• -nt: Number of threads (default is 8)
• -nw: Number of windows (default is 400)

官方demo

部分结果解释

Coverage across reference

Coverage Histogram

Genome Fraction Coverage

Duplication Rate Histogram

Mapped Reads Nucleotide Content

Mapped Reads GC-content Distribution

Mapped Reads Clipping Profile

Homopolymer Indels

Mapping Quality Across Reference

Mapping Quality Histogram

Insert Size Across Reference

Insert Size Histogram

RNA-seq QC

qualimap rnaseq -bam kidney.bam -gtf human.64.gtf -outdir rnaseq_qc_results

Reads Genomic Origin

Coverage Profile Along Genes (Total)

Coverage Histogram (0-50X)

Junction Analysis

Multisample BAM QC（with groups）

qualimap multi-bamqc -i gh2ax_chip_seq.txt -outdir gh2ax_multibamqc

PCA

Coverage Across Reference

Coverage Histogram (0-50X)

Genome Fraction Coverage

Duplication Rate Histogram

Mapped reads GC-content

Mapped Reads Clipping Profile

Mapped Reads GC-content Distribution

Mapping Quality Across Reference

Mapping Quality Histogram

Counts QC（with group）

qualimap counts -d GlcN_countsqc_input.txt -c -s mouse -outdir glcn_mice_counts

Rscript /ssd1/wy/.conda/envs/qualimap/share/qualimap-2.2.2d-2/scripts/countsQC.r --homedir /ssd1/wy/.conda/envs/qualimap/share/qualimap-2.2.2d-2/scripts --input /tmp/qualimap1681982390627//input.txt -k 5 --info /ssd1/wy/.conda/envs/qualimap/share/qualimap-2.2.2d-2/species/mouse.ens68.txt --compare -o /tmp/qualimap1681982390627/
Reading input data using input description from /tmp/qualimap1681982390627//input.txt 

Counts Density

Scatterplot Matrix

Saturation

Counts Distribution

Features With Low Counts

Counts QC（single）

Saturation

Bio Detection

Counts Per Biotype

Length Bias

GC Bias