#CP3RJSMF0 Hello, I am going to try the #CP3RJSMF0 pipeline with a sample that was obtained by targeted amplification of bisulphite converted DNA from several participants. The amplicons have been tagged and illumina sequenced. Should I use these options in the command line "--target_regions_file genome_target_regions.bed \ --collecthsmetrics"? and can you give me an example of the .bed file? Cheers, Mirko

Hi @Mirko Pegoraro - in short: yes See the docs: https://nf-co.re/methylseq/4.2.0/docs/usage/#targeted-sequencing-optional I'm fairly confident that it's a very simple BED file, eg. 3 columns: chrom, start, end