Description of feature
In the nf-core/cutandrun pipeline, the minimum_alignment_q_score parameter (default: 20) allows explicit filtering of low-quality alignments based on MAPQ scores. However, this option is not implemented in nf-core/chipseq, despite being a common QC step for ChIP-seq data.
This was discussed in the nf-core Slack, and the team suggested opening an issue for tracking. @JoseEspinosa
Description of feature
In the nf-core/cutandrun pipeline, the minimum_alignment_q_score parameter (default: 20) allows explicit filtering of low-quality alignments based on MAPQ scores. However, this option is not implemented in nf-core/chipseq, despite being a common QC step for ChIP-seq data.
This was discussed in the nf-core Slack, and the team suggested opening an issue for tracking. @JoseEspinosa