SsvQC: an integrated CUT&RUN quality control workflow for histone modifications and transcription factors.

ABSTRACT:

Objective

Among the different methods to profile the genome-wide patterns of transcription factor binding and histone modifications in cells and tissues, CUT&RUN has emerged as a more efficient approach that allows for a higher signal-to-noise ratio using fewer number of cells compared to ChIP-seq. The results from CUT&RUN and other related sequence enrichment assays requires comprehensive quality control (QC) and comparative analysis of data quality across replicates. While several computational tools currently exist for read mapping and analysis, a systematic reporting of data quality is lacking. Our aims were to (1) compare methods for using frozen versus fresh cells for CUT&RUN and (2) to develop an easy-to-use pipeline for assessing data quality.

Results

We compared a w

SUBMITTER: Boyd J 

PROVIDER: S-EPMC8454122 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature