Abstract
The COMPSRA and exceRpt pipelines that are used explicitly for quantifying RNAseq data were compared and evaluated in this study. In both pipelines, various tools are used to extract various kinds of RNAs from a given sample. Small RNA sequencing data from milk somatic cell samples from 12 buffaloes were compared using the COMPSRA and exceRpt analyses. The two selected pipelines were also evaluated from a variety of angles, including the length of time required for comparing the sequences, the types of supported databases for annotation, and the number of distinct RNAs produced as results. The output varies even though the pipelines are used for similar purposes, because different quantification techniques are used for transcriptomic data. When the two pipelines were compared, it became clear that both had drawbacks. For example, exceRpt's analysis time was very high, while COMPSRA's count of generated specific RNA was lower. In contrast to exceRpt, which detected abundance of tRNA, rRNA, miRNA, snRNA, snoRNA, and lncRNA, COMPSRA found circRNA and piRNA to have a higher level of diversity and abundance.
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