Running Trinity on your own data:

First, create a file 'samples.txt' with the following format:

condition(tab)replicate(tab)left.fq(tab)right.fq(tab) ...

For example, if I had just 2 conditions with each having 2 bio replicates, my samples.txt file might look like so:

condA    condA_rep1    condA_rep1_1.fastq.gz     condA_rep1_2.fastq.gz
condA    condA_rep2    condA_rep2_1.fastq.gz     condA_rep2_2.fastq.gz
condB    condB_rep1    condB_rep1_1.fastq.gz     condB_rep1_2.fastq.gz
condB    condB_rep2    condB_rep2_1.fastq.gz     condB_rep2_2.fastq.gz

Once you have your samples.txt file, you can then run Trinity like so.

FIRST!!!! Let's do this:

Start a screen session

%  screen -S myTrinity

Then, for some weird reason.... we need to set the environmental variable... screen related:

%  export LD_LIBRARY_PATH=/usr/local/lib

and then run Trinity:

$TRINITY_HOME/Trinity --samples_file  samples_file.txt \
    --CPU 6 --max_memory 10G --seqType fq --output my_trinity_outdir \
    2>&1 | tee run_trinity.log

If based on your fastqc results, it's clear that you will benefit from quality trimming, feel free to include the parameter '--trimmomatic'