QC

Methylation distribution

methylation_matrix='path/to/methylation_matrix.tsv'
circula qc -s 1 ${methylation_matrix} -o ./methyaltion_dist.png

Fragment length distribution

The --clip-r1 and --clip-r2 flags are optional and should be identical to the adapter trimming step.

bam_input1='path/to/test_fragment_length1.bam'
bam_input2='path/to/test_fragment_length2.bam'
# Plot fragment length distribution for single bam file
circula qc -s 2 -o ./output/frag_dist.png -@ 5 --title 'test_fragment_dist' --clip-r1 10 --clip-r2 10 ${bam_input1}
# Plot average fragment length distribution for multiple bam files
circula qc -s 2 -o ./output/frag_dist.png -@ 5 --title 'test_fragment_dist' --clip-r1 10 --clip-r2 10 ${bam_input1} ${bam_input2}

Dinucleotide frequency

Reference -r is required for dinucleotide frequency calculation. The -f flag is required to specify the fragment length for dinucleotide frequency calculation. The --clip-r1 and --clip-r2 flags are optional and should be identical to the adapter trimming step.

ref = 'path/to/reference_genome.fa'
bam_input1='path/to/test_dinucleotide_frequqncy1.bam'
bam_input2='path/to/test_dinucleotide_frequqncy2.bam'
# check dinucleotide frequency for all 167bp fragments, multiple samples.
circula qc -s 3 -f 166 -o ./output/dinucleotide_frequency_dist.png -@ 8 -r ${ref} --clip-r1 10 --clip-r2 10 ${bam_input1} ${bam_input2}