What is the recommended length of reads in CUT&RUN sequencing?

We sequence 50bp for our in-house CUT&RUN tests. The size of CUT&RUN DNA is typically 40-200bp. If the read is 75bp or 100bp long, a portion of the CUT&RUN DNA (for those < 75bp or 100bp) will contain the adaptor sequence in the reads and therefore lead to trouble in the read trimming process. If the adaptor sequence can't be trimmed completely, the reads that contain the adaptor sequence won't be mapped back to the genome and you will lose the diversity of your reads.

Last updated: March 15, 2023