Are the indices in line with read 1? They are also shorter than what our sequencing facility normally uses, are they hard to demultiplex?
We developed a tool for demultiplexing libraries with complex barcoding (including in-line barcodes), as is the case of iCLIP. The tool is called Ultraplex, it's fast and easy to use, please find here: https://wellcomeopenresearch.org/articles/6-141. See Fig1 for an example read from a typical iCLIP library, and the demultiplexing workflow. This tool is also implemented within https://imaps.goodwright.com/, a free platform for password-protected data analysis dedicated especially to CLIP.