Evaluating Detection of small RNA derived fragments from small RNA-seq data
An increasing amount of evidence indicates that fragments derived from longer small RNAs such as snoRNAs, snRNAs, and rRNAs may hold functions relevant to biology and disease. However, they remain poorly understood. Few pipelines exist to analyze the fragmentation of small RNAs, and even fewer take users from raw reads to processed results. Every decision that a user makes when processing small RNA-seq data can greatly impact downstream results. Thus, we sought to develop sRNAfrag, a standardized workflow that can accurately quantify and describe the presence of sRNA fragments, with three inputs: run data, a reference genome, and an annotation file. Overall design: Nine total cell lines were sequenced, including HMEC (n = 1), SK-N-SH (n = 2), IMR32 (n = 2), T47D (n = 2), and HCC1143 (n = 2) to evaluate the detection of small RNA derived fragments with our new pipeline, sRNAfrag. Here we report the results of counts obtaned from snoRNA fragments (sd).