This repository contains bioinformatic workflows used in gray whale expressions paper. The workflows are written with Workflow Description Language http://www.openwdl.org/ For each of the workflow example inputs (as json) are give, to reproduce the research - download the samples and change the pathes to correspond to those on your file system.
Workflows for Longevity Associated Genes analysis are at workflows/annotate/transcripts There first indexes are build with vsearch_index.wdl and then aligments to LAGs are done.
Coding genes comparisonds are done at at workflows/annotate/transcripts At first ORFs are extracted and proteins are predicted with Transdecoder Then Diamond was used to align predicted proteins to Uniref90 clusters