cuffdiff /depot/bioinfo/data/Projects/Taylor_Rabbit/data/reference/Oryctolagus_cuniculus.OryCun2.0.95.gtf -p 19 -L CH,LH \
/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_CH34/STAR/CH34_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_CH35/STAR/CH35_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_CH36/STAR/CH36_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_CH37/STAR/CH37_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_CH38/STAR/CH38_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_CH39/STAR/CH39_sortedbypos.bam \
/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_LH26/STAR/LH26_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_LH28/STAR/LH28_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_LH29/STAR/LH29_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_LH30/STAR/LH30_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_LH31/STAR/LH31_sortedbypos.bam,/depot/bioinfo/data/Projects/Taylor_Rabbit/results/RNA-seq_pipeline/output/mapping_LH32/STAR/LH32_sortedbypos.bam \
 -o cuffdiff_out_LHvsCH

