Running the actual assemblyΒΆ

Now we’ll assemble all of these reads into a transcriptome, using the Trinity de novo transcriptome assembler.

First, install some prerequisites for Trinity:

sudo apt-get -y install bowtie samtools zlib1g-dev ncurses-dev

Next, install Trinity v2.2.0:

curl -L > trinity.tar.gz
tar xzf trinity.tar.gz
mv trinityrnaseq* trinity/

cd trinity

Go into the work directory, and prepare the data:

cd /mnt/work
for i in *.dn.fq.gz
do $i

cat *.1 > left.fq
cat *.2 > right.fq

Now, run the Trinity assembler:

~/trinity/Trinity --left left.fq --right right.fq --seqType fq --max_memory 10G --bypass_java_version_check

This will give you an output file trinity_out_dir/Trinity.fasta.

Let’s copy that to a safe place, where we’ll work with it moving forward:

cp trinity_out_dir/Trinity.fasta rna-assembly.fa

Next: Assembly statistics and evaluation

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