ls */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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -o merged_asm -g /data/results/reference/hg19/Homo_sapiens.GRCh38.84.chr.gtf2.to_hg19  assemblies.txt


#/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
#reczko@max:/data/images/proton/run44/mm10/tophat_005$ samtools reheader /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.dict sort_uniq.bam > sort_uniq.bam2
#reczko@max:/data/images/proton/run44/mm10/tophat_005$ cd ../tophat_006
#reczko@max:/data/images/proton/run44/mm10/tophat_006$ samtools reheader /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.dict sort_uniq.bam > sort_uniq.bam2
#/data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf


cuffdiff -L CON,DOX --no-effective-length-correction --library-type fr-secondstrand --no-update-check --num-threads 9 -q -o cuffdiff_CON_vs_DOX  merged_asm/merged.gtf PHR15-CON1.bam2,PHR16-CON2c.bam2 PHR17-DOX1c.bam2,PHR18-DOX2.bam2 &> cuffdiff_CON_vs_DOX.log

#awk -f /data/results/tools/rnaseq/get-xloc-tcons-oID-from-merged1.awk /data/images/proton/run276/www/merged_asm/merged.gtf > /data/images/proton/run276/www/merged_asm/merged.gtf.ids
reczko@max:/data/images/proton/run276/www/merged_asm$ awk -v ref="/data/results/reference/hg19/Homo_sapiens.GRCh38.84.chr.gtf2.to_hg19.bt" -f /data/results/tools/rnaseq/get-xloc-tcons-oID-biotype-from-merged1.awk merged.gtf |uniq > merged.gtf.bt

awk -f /data/results/tools/rnaseq/get-biotypes-for-isoforms1.awk isoform_exp.diff > isoform_exp.diff.csv