Sleuth Object (S.avenae winged/unwinged)

Differential gene expression analysis where RNA sequencing reads from the <i>Sitobion avenae</i> were pseudoaligned to the reference transcriptome with Kallisto¹. Samples from winged aphids were compared to samples from unwinged aphids using Sleuth². The sleuth object (generated with version 0.30.0) can be used with sleuth_live() to examine the expression at a transcript level.<br>Details on installation of Sleuth can be found at https://github.com/pachterlab/sleuth.<br>Once Sleuth is installed in R then simply read in the sleuth object and run sleuth live as follows:<br>library(sleuth)sleuthObject sleuth_live(sleuthObject) <br><br>¹Bray, N.L., Pimentel, H., Melsted, P. and Pachter, L., 2016. Near-optimal probabilistic RNA-seq quantification. <i>Nature biotechnology</i>, <i>34</i>(5), pp.525-527.<br><br>²Pimentel, H., Bray, N.L., Puente, S., Melsted, P. and Pachter, L., 2017. Differential analysis of RNA-seq incorporating quantification uncertainty. <i>Nature methods</i>, <i>14</i>(7), p.687.

本数据集为差异基因表达分析研究，将麦长管蚜（*Sitobion avenae*）的RNA测序读数通过Kallisto工具伪比对至参考转录组¹。采用Sleuth工具²对有翅蚜样本与无翅蚜样本开展差异表达比较。本研究生成的sleuth对象（版本号0.30.0）可通过`sleuth_live()`函数在转录本层面进行表达量分析。Sleuth工具的安装详情可访问链接：https://github.com/pachterlab/sleuth。若已在R环境中完成Sleuth安装，仅需按如下代码读取并运行sleuth对象：
`library(sleuth)`
`sleuthObject <- sleuth_live(sleuthObject)`

¹ Bray, N.L.、Pimentel, H.、Melsted, P. 与 Pachter, L.，2016年。《近乎最优的概率型RNA测序定量方法》，*Nature Biotechnology*，第34卷第5期，第525-527页。

² Pimentel, H.、Bray, N.L.、Puente, S.、Melsted, P. 与 Pachter, L.，2017年。《整合定量不确定性的RNA测序差异表达分析》，*Nature Methods*，第14卷第7期，第687页。