#June 7, 2012
#From Wen Jing &Zhang kunshan
For RNA seq data:tophat -C -Q -o /data/raw_data/jinying-2012-04-12/result/g30/ -p 30 -g 10 --library-type fr-secondstrand --coverage-search bowtie-0.12.7/indexes/mm9_c /data/raw_data/jinying-2012-04-12/g30/solid138000556_20120412_2_g30_F3.csfasta /data/raw_data/jinying-2012-04-12/g30/solid138000556_20120412_2_g30_F3_QV.qual
cufflinks-1.1.0.Linux_x86_64/cufflinks -p 30 -b /data/genome+ref/mmu9-chromFa/mmu9.fa -M /data/genome+ref/annotation/mm9.F_rtRNA.gtf --library-type fr-secondstrand -u -I 10000000 -o /data/raw_data/jinying-2012-04-12/result/g31 -G /data/genome+ref/annotation/mmu-refGene20120304.gtf /data/raw_data/jinying-2012-04-12/result/g31/accepted_hits.bam
cut -f 4,10 /data/raw_data/jinying-2012-04-12/result/g82/genes.fpkm_tracking >/data/raw_data/jinying-2012-04-12/result/g82/g82.txt
sort /data/raw_data/jinying-2012-04-12/result/g30/g30.txt -o /data/raw_data/jinying-2012-04-12/result/g30/g30.txt
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