Running the actual assemblyΒΆ
Now we’ll assemble all of these reads into a transcriptome, using the Trinity de novo transcriptome assembler.
We’ve already installed the prerequisites (see Installation of base image); now, install Trinity v2.2.0 itself:
cd
curl -L https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.2.0.tar.gz > trinity.tar.gz
tar xzf trinity.tar.gz
mv trinityrnaseq* trinity/
cd trinity
make
Go into the work directory, and prepare the data:
cd /mnt/work
for i in *.dn.fq.gz
do
split-paired-reads.py $i
done
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 5G --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
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