Are quality filtered reads required to create your own error model?

[o-william-white]

Hello,

I would like to create my own error model. In the example below, should reads_R1.fastq.gz and reads_R2.fastq.gz be quality filtered prior to mapping?

Best wishes Ollie

bowtie2-build genomes.fasta genomes
bowtie2 -x genomes -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz | \
samtools view -bS | samtools sort -o genomes.bam
samtools index genomes.bam