/home/liuhui/bin/trinityrnaseq_r20140413p1/util/support_scripts/get_Trinity_gene_to_trans_map.pl Trinity.fasta > Trinity.fasta_trans_map
bowtie-build Trinity.fasta Trinity.fasta.bowtie
rsem-prepare-reference --no-polyA --no-bowtie --transcript-to-gene-map Trinity.fasta_trans_map Trinity.fasta Trinity.fasta.RSEM
mkdir -p lib
cd lib
bowtie -q --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 Trinity.fasta.bowtie -1 left.fq -2 right.fq | samtools view -S -b -o bowtie.bam -
rsem-calculate-expression --paired-end -p 4 --keep-intermediate-files --forward-prob 0 --bam bowtie.bam Trinity.fasta.RSEM RSEM
samtools sort bowtie.bam bowtie.csorted
samtools index bowtie.sorted.bam
