rsem to generate expression

By and large, gene expression can be generated by DESeq2 or EBseq. incidentally DESeq2 refered to repeat samples,by contrary, EBSeq
non-repeated.nevertheless, what if you want to calculte expression from specific sample with reference of Unigene fa file, the 
rsem software shoud be used.

Initially, installing rsem befor you should install bowtie first.and then type below command to install rsem:
git clone git@github.com:bli25ucb/RSEM_tutorial.git ./
unzip bowtie2-2.2.6-source.zip
cd bowtie2-2.2.6
make -j 8
cd ..
tar -xzf RSEM-1.2.25.tar.gz
cd RSEM-1.2.25
make -j 8
make ebseq
cd ..
cd ..

Usage:
Step1,building reference from unigene fa or genome fa showed below:
/opt/biosoft/rsem/current/rsem-prepare-reference All_gene.fa test --bowtie note:test for prefix of file,inputed file was All_gene.fa
attention:--bowtie parameter must be given.
Result files:
All_gene.fa  test.1.ebwt  test.3.ebwt  test.grp     test.n2g.idx.fa  test.rev.2.ebwt  test.ti
run.sh       test.2.ebwt  test.4.ebwt  test.idx.fa  test.rev.1.ebwt  test.seq         test.transcripts.fa
/opt/biosoft/rsem/current/rsem-calculate-expression --paired-end T01_good_1.fq T01_good_2.fq ../fa_file/test samplename note:prefix of samplename
Result file:
T01_good_1.fq  nohup.out  samplename.genes.results     samplename.stat            samplename.transcript.sorted.bam
T01_good_2.fq  run.sh     samplename.isoforms.results  samplename.transcript.bam  samplename.transcript.sorted.bam.bai
result from samplename.genes.results file