Here is a blog that gives excellent Trinity instructions:
https://cartwrightlab.wikispaces.com/RNAseq+Assembly+in+Trinity

#for paired end reads, combine each side of pairs into one file

cat pair.DR004_Artibeus_Jamaicensis_MOE_ACAGTG_L001_R1* >> Arjam_MOE_R1.fq

cat pair.DR004_Artibeus_Jamaicensis_MOE_ACAGTG_L001_R2* >> Arjam_MOE_R2.fq

#run a trimming script

python ~/Scripts/q-trim.py Arjam_MOE_R1.fq Arjam_MOE_R1_trim.fq

#woops I run into this error:

importerror no module named screed

#it looks like I need the "screed" module for this; looks like I also need to update "setup tools"

#first install pip

sudo python get-pip.py

pip install ipython #not sure what this did

#still missing the screed module

sudo pip install setuptools --upgrade

sudo pip install git+https://github.com/ged-lab/screed.git

#okay seems to be working now

#trimmed with the default setting in which a minimum Qscore = 5

#minimum length = 30; lets see how this works

python ~/Scripts/q-trim.py Arjam_MOE_R1.fq Arjam_MOE_R1_trim.fq

python ~/Scripts/q-trim.py Arjam_MOE_R2.fq Arjam_MOE_R2_trim.fq

#now i need to assemble paired reads--extracting only the pairs using both.py

python ~/Scripts/both.py Arjam_MOE_R1_trim.fq Arjam_MOE_R2_trim.fq

#this creates two files ...R1_trim.fq.both and R2_trim.fq.both

#this script took about one hour to run

#finally time to run trinity!

Trinity.pl --seqType fq --left Arjam_MOE_R1_trim.fq.both --right Arjam_MOE_R2_trim.fq.both --CPU 4 --JM 20G --output trinity_output/

Everything is up and running now. Stay tuned.