README.md

transcriptomeProcessing

This repository contains scripts or slurm batch files that were used to process transcriptome data (follows Trinity tutorials, adjusted for our data)

Clean, assemble, annotate

First, clean the reads

runTrimGalore.sh

Next, move and rename

moveAndRename.batch.sh (uses moveandrename.sh)

For trinity, concatenate reads so that can run on all libraries from a single species

cat.batch.sh (uses catForTrinity.sh)

Run trinity, adjust for memory depending on size of input

runTrinityC*.sh

Run trinotate and a few stats (run within every species own trinity folder)

runTrinotate.sh runSomeStats.sh

Differential expression