19 | | * Check adapter contamination with fastqc. Remove adapters with cutadapt or trim_galore. Since many ATAC-seq experiments use the Nextera DNA Library Prep Kit, one commonly needs to trim Nextera adapters. |
20 | | |
21 | | {{{ |
22 | | # --fastqc Run FastQC in the default mode on the FastQ file once trimming is complete. |
23 | | # --nextera Nextera adapter is commonly used for ATAC-seq |
24 | | Adapter sequence to be trimmed is the first 12bp of the Nextera adapter |
| 19 | * Check adapter contamination with fastqc. Remove adapters with cutadapt or trim_galore. |
| 20 | |
| 21 | {{{ |
| 22 | # --fastqc Run FastQC in the default mode on the fastq file once trimming is complete. |
| 23 | # --nextera Adapter sequence to be trimmed is the first 12bp of the Nextera adapter |