/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cuffmerge -p 8 -s /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa -o merged_asm -g /data/results/reference/mmu/mm10/Mus_musculus.GRCm38.84.last500nt.gtf2 assemblies.txt
gtf_to_sam -F GK3R1-T1/accepted_hits3/transcripts.gtf merged_asm/tmp/gtf2sam_fileBSjH9N