Low library yields are unavoidable in some experiments (e.g. mapping a low abundance target and/or using low cell numbers). For low-concentration libraries, consider the following options:
Repeat library prep: Use more CUT&RUN-enriched DNA input and/or increase the number of PCR cycles used for indexing PCR to improve yields for sequencing. Note that increasing the number of PCR cycles may lead to higher read duplication rates and require deeper sequencing to capture read diversity.
Concentrate library for sequencing: If library prep cannot be repeated, use a Speedvac to increase the library concentration and add as much of the library as possible to the sequencing pool. Deeper sequencing is recommended to ensure sufficient read depth for the the low-concentration library.
In both cases, deeper sequencing is strongly recommended.