/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cuffmerge -p 8 -s /data/results/reference/hsa/GRCh37/human_g1k_v37.fasta -o merged_asm_scan -g /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf assemblies_scan.txt
gtf_to_sam -F SCAN-tr-0h-a/accepted_hits_ensembl_novel/transcripts.gtf merged_asm_scan/tmp/gtf2sam_file0WbRIF
gtf_to_sam -F SCAN-tr-0h-b/accepted_hits_ensembl_novel/transcripts.gtf merged_asm_scan/tmp/gtf2sam_file88mIbY
gtf_to_sam -F SCAN-tr-1h-a/accepted_hits_ensembl_novel/transcripts.gtf merged_asm_scan/tmp/gtf2sam_fileEz5mw6
gtf_to_sam -F SCAN-tr-1h-b/accepted_hits_ensembl_novel/transcripts.gtf merged_asm_scan/tmp/gtf2sam_fileKEcbj4
gtf_to_sam -F SCAN-tr-3h-a/accepted_hits_ensembl_novel/transcripts.gtf merged_asm_scan/tmp/gtf2sam_fileKCOICR
gtf_to_sam -F SCAN-tr-3h-b/accepted_hits_ensembl_novel/transcripts.gtf merged_asm_scan/tmp/gtf2sam_fileMXVfgv
gtf_to_sam -F SCAN-untr-0h-a/accepted_hits_ensembl_novel/transcripts.gtf merged_asm_scan/tmp/gtf2sam_fileYlxizZ
gtf_to_sam -F SCAN-untr-0h-b/accepted_hits_ensembl_novel/transcripts.gtf merged_asm_scan/tmp/gtf2sam_file8SoK4i
sort -k 3,3 -k 4,4n --temporary-directory=merged_asm_scan/tmp/ merged_asm_scan/tmp/gtf2sam_file0WbRIF merged_asm_scan/tmp/gtf2sam_file88mIbY merged_asm_scan/tmp/gtf2sam_fileEz5mw6 merged_asm_scan/tmp/gtf2sam_fileKEcbj4 merged_asm_scan/tmp/gtf2sam_fileKCOICR merged_asm_scan/tmp/gtf2sam_fileMXVfgv merged_asm_scan/tmp/gtf2sam_fileYlxizZ merged_asm_scan/tmp/gtf2sam_file8SoK4i > merged_asm_scan/tmp/mergeSam_fileABb8bt
cufflinks -o merged_asm_scan/ -F 0.05 -g /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 merged_asm_scan/tmp/mergeSam_fileABb8bt
cuffcompare -o tmp_meta_asm -C -G  -r /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf  -s /data/results/reference/hsa/GRCh37/human_g1k_v37.fasta merged_asm_scan//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf  -s /data/results/reference/hsa/GRCh37/human_g1k_v37.fasta merged_asm_scan//merged.gtf