====== Upgrade Trinity + RSEM ======

* Upgrade Trinity
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<code>
cd /root/
wget  http://garr.dl.sourceforge.net/project/trinityrnaseq/trinityrnaseq_r20131110.tar.gz 
tar xzf trinityrnaseq_r20131110.tar.gz 
cd trinityrnaseq_r20131110/ 
make

cd ..
mv /usr/share/trinity /usr/share/trinityOLD
mv trinityrnaseq_r20131110 /usr/share/trinity 
chown -R root:root /usr/share/trinity
chmod -R 755 /usr/share/trinity
</code>
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* Install RSEM
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<code>
cd /root/
wget  http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.7.tar.gz  
tar -xvzf rsem-1.2.7.tar.gz 
cd rsem-1.2.7/  
make

cd ..
mv rsem-1.2.7 /usr/local/bin/  
chown -R root:root /usr/local/bin/rsem-1.2.7 
cd /usr/local/bin/
ln -s rsem-1.2.7 rsem 
</code>
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* User script to activate Trinity and RSEM
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<code bash>
export PATH=/usr/share/trinity:/usr/share/trinity/util:/usr/share/trinity/util/RSEM_util:/usr/local/bin/rsem:$PATH
export TRINITY_HOME=/usr/share/trinity
ulimit -s unlimited 
</code>
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* Test installation
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Logon and activate Trinity
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<code>
user@rachaelx:~$ source trinityactivate.sh
</code>
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Copy sample directory
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<code>
user@rachaelx:~$ cp -R /usr/share/trinity/sample_data ~/
</code>
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Edit test script and remove script path
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<code>
user@rachaelx:~$ cd sample_data/test_Trinity_Assembly/
user@rachaelx:~/sample_data/test_Trinity_Assembly$ nano -w runMe.sh
</code>
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<code bash>
#!/bin/bash -ve

if [ -e reads.left.fq.gz ] && ! [ -e reads.left.fq ]
then
    gunzip -c reads.left.fq.gz > reads.left.fq
fi
if [ -e reads.right.fq.gz ] && ! [ -e reads.right.fq ]
then
    gunzip -c reads.right.fq.gz > reads.right.fq
fi

#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

## use jellyfish
Trinity.pl --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup
##### Done Running Trinity #####

if [ ! $* ]; then
    exit 0
fi
sleep 2

######################################################
## align reads back to the transcripts using Bowtie ##
######################################################

sleep 2
alignReads.pl --left reads.left.fq --right reads.right.fq --target trinity_out_dir/Trinity.fasta --aligner bowtie --seqType fq --SS_lib_type RF
##### Done aligning reads #######
sleep 2

###########################################
# use RSEM to estimate read abundance  ####
###########################################

sleep 2
run_RSEM.pl --transcripts trinity_out_dir/Trinity.fasta --name_sorted_bam bowtie_out/bowtie_out.nameSorted.sam.+.sam.PropMapPairsForRSEM.bam --paired
###### Done running RSEM ########

</code>
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Exec test
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<code>
user@rachaelx:~/sample_data/test_Trinity_Assembly$ ./runMe.sh
</code>
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Result
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<code>
...
##### Done Running Trinity #####
</code>
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Clean test dirs
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<code>
user@rachaelx:~/sample_data/test_Trinity_Assembly$ ./cleanme.pl
</code>
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