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.