In paired-end eCLIP experiments, Read 2 is extracted based on enrichment of crosslink termination sites. Clipper peaks called on these reads are complementary to cDNA (sense to cross-linked RNA). Following the seCLIP protocol in Blue et al., 2022, it seems that Read 1 would be complementary to cross-linked RNA. Should the reverse_strand argument be passed to call_peaks in order to account for this? Thanks
In paired-end eCLIP experiments, Read 2 is extracted based on enrichment of crosslink termination sites. Clipper peaks called on these reads are complementary to cDNA (sense to cross-linked RNA). Following the seCLIP protocol in Blue et al., 2022, it seems that Read 1 would be complementary to cross-linked RNA. Should the reverse_strand argument be passed to call_peaks in order to account for this? Thanks