#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 WT_6h_replicate_IIb -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/WT_6h_replicate_II.fastq
/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o WT_IFN-gamma_replicate_Ib -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/WT_IFN-gamma_replicate_I.fastq
/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o WT_IFN-gamma_replicate_IIb -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/WT_IFN-gamma_replicate_II.fastq
/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o WT_IL4_replicate_Ib -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/WT_IL4_replicate_I.fastq
/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat --transcriptome-only -p 10 -n 2 -o WT_IL4_replicate_IIb -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C  /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/WT_IL4_replicate_II.fastq