SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
Currently, exons are named with an integer ID (see here), which is problematic because 1. the IDs are not externally meaningful, and 2. subtle differences between annotation versions would result in many of the same exons receiving different IDs between versions. We might consider assigning exonMap$Geneid for exon rownames instead.
Currently, exons are named with an integer ID (see here), which is problematic because 1. the IDs are not externally meaningful, and 2. subtle differences between annotation versions would result in many of the same exons receiving different IDs between versions. We might consider assigning
exonMap$Geneidfor exon rownames instead.