Open jdidion opened 8 years ago
In some applications, it is necessary to hard-clip the 3' end of reads regardless of quality or overall read length. A key example of this is bisulfite sequencing: the 2 3' bases of read 2 are biased due to the end repair process (https://sequencing.qcfail.com/articles/library-end-repair-reaction-introduces-methylation-biases-in-paired-end-pe-bisulfite-seq-applications/). I added an option (--clip) that performs hard-clipping after adapter trimming but before any quality trimming.
In some applications, it is necessary to hard-clip the 3' end of reads regardless of quality or overall read length. A key example of this is bisulfite sequencing: the 2 3' bases of read 2 are biased due to the end repair process (https://sequencing.qcfail.com/articles/library-end-repair-reaction-introduces-methylation-biases-in-paired-end-pe-bisulfite-seq-applications/). I added an option (--clip) that performs hard-clipping after adapter trimming but before any quality trimming.