CLC_workflow

The first step is reading the fastq file.

The reads are then processed for trimming, with the following parameters:

• If NlaIII and DpnII libraries have been separately barcoded, the procedure is applied to both fastq files independently
• The sequence of NlaII adapter is "CATG"
• The sequence of DpnII adapter is "GATC"

The trimmed sequence are then mapped to reference genome using these parameters:

• again, if NlaIII and DpnII libraries have been separately barcoded, the NlaIII and DpnII reads are mapped independently