For this exercise you need to be logged in to Uppmax.
Setup the folder structure:
source ~/git/GAAS/profiles/activate_rackham_env
export data=/proj/g2019006/nobackup/$USER/data
export RNAseq_assembly_path=/proj/g2019006/nobackup/$USER/RNAseq_assembly
Trinity assemblies can be used as complementary evidence, particularly when trying to polish a gene build with Pasa. Before you start, check how big the raw read data is that you wish to assemble to avoid unreasonably long run times.
cd $RNAseq_assembly_path
mkdir trinity
cd trinity
module load trinity/2.4.0
module load samtools/1.9
Trinity --seqType fq --max_memory 32G --left $data/raw_computes/ERR305399_1.fastq.gz --right $data/raw_computes/ERR305399_2.fastq.gz --CPU 5 --output trinity --SS_lib_type RF
Trinity takes a long time to run (several hours), you can stop the program when you start it and have a look at the results, look in $data/RNAseq/trinity the output is Trinity.fasta
Tips: Using Trinity in genome annotation
Some advantages :
Some disadvantage :