Rui:Cufflinks 11.7.11
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Cufflinks_11.7.11 w/ G annotation[edit]
- Previously, I used -g option which allows reference as the guide
- Dr. Zhang used -G option which excludes any novel transcripts
- To repeat cufflinks in genome-miner by using the following command
nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx13 /home/ruiliu/RNAseq/Hiseq111005/tophat/Indx13_accepted_hits.bam > Indx13.log&
Problem need to solve: # can .bam file directly used for cufflinks? # is the tracking_id exactly same as gene_id?
--- genome-minor, bam file worked!
mkdir ~/RNAseq/Hiseq111005/cufflinks-G nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx13 /home/ruiliu/RNAseq/Hiseq111005/tophat/Indx13_accepted_hits.bam > Indx13.log& nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx14 /home/ruiliu/RNAseq/Hiseq111005/tophat/Indx14_accepted_hits.bam > Indx14.log& nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx15 /home/ruiliu/RNAseq/Hiseq111005/tophat/Indx15_accepted_hits.bam > Indx15.log&
--- meangenemachine, bam file failed again!
nohup cufflinks -G ~/iGenome/ ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx13_cufflinks ~/Hiseq111005/Indx13/Indx13_tophat-G/accepted_hits.bam > Indx13.log&