HITS-CLIP data analyses

Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor and removing low-quality bases, and too short reads (less than 13 nucleotides) were also dropped. FASTX-Toolkit (version 0.0.13) was used to obtain a clean set of reads. Clean reads were mapped to the GRCm38.p3 version of the mouse genome by TopHat2 (46). After removing duplicate reads, the remainder was used for subsequent analyses.

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