ls 4*/accepted_hits/transcripts.gtf > assemblies.txt
PATH=/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64:$PATH; export PATH
/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cuffmerge   -p 8 -s /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -o merged_asm -g /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Archives/archive-2013-03-06-15-01-24/Genes/genes.gtf  assemblies.txt

cuffdiff -L Hum,Sal --no-effective-length-correction --library-type fr-secondstrand --no-update-check --num-threads 8 -q -o cuffdiff_Hum_vs_Sal  merged_asm/merged.gtf 43819Hum.bam2,43823Hum.bam2  4382Sal.bam2,4383Sal.bam2  &> cuffdiff_Hum_vs_Sal.log