#PATH=/data/results/tools/align/bowtie-1.2.1.1:$PATH; export PATH
PATH=/data/results/tools/align/bowtie-0.12.9:$PATH; export PATH

#/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o a -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/
#/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o wt0hrep1d -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/0hrep1b.fastq

/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o KO_0h_replicate_Ib -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/KO_0h_replicate_I.fastq
/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o KO_0h_replicate_IIb -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/KO_0h_replicate_II.fastq
/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o KO_2h_replicate_Ib -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/KO_2h_replicate_I.fastq
/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o KO_2h_replicate_IIb -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/KO_2h_replicate_II.fastq
/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o KO_6h_replicate_Ib -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/KO_6h_replicate_I.fastq