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

Next, install Trinity v2.0.6:

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, which you can get stats on like so:

curl -L -O
python 300 trinity_out_dir/Trinity.fasta

Change the filename and rename all the sequences:

gzip -c trinity_out_dir/Trinity.fasta > trinity-nematostella-raw.fa.gz
curl -O
chmod u+x
./ nema trinity-nematostella-raw.fa.gz

This last command will give you trinity-nematostella-raw.renamed.fasta.gz, which contains all of the renamed sequences.

Next: BLASTing your assembled data

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