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====cufflinks 10.28.11==== * Meangenemachine nohup samtools view -h ../Indx7_tophat-G/accepted_hits.bam > accepted_hits.sam & nohup samtools view -h ../Indx8_tophat-G/accepted_hits.bam > accepted_hits.sam & nohup samtools view -h ../Indx9_tophat-G/accepted_hits.bam > accepted_hits.sam & nohup samtools view -h ../Indx10_tophat-G/accepted_hits.bam > accepted_hits.sam & nohup samtools view -h ../Indx11_tophat-G/accepted_hits.bam > accepted_hits.sam & nohup samtools view -h ../Indx13_tophat-G/accepted_hits.bam > accepted_hits.sam & nohup samtools view -h ../Indx14_tophat-G/accepted_hits.bam > accepted_hits.sam & nohup samtools view -h ../Indx15_tophat-G/accepted_hits.bam > accepted_hits.sam & cd ~/Hiseq111005/Indx7/Indx7_cufflinks cd ~/Hiseq111005/Indx8/Indx8_cufflinks cd ~/Hiseq111005/Indx9/Indx9_cufflinks cd ~/Hiseq111005/Indx10/Indx10_cufflinks cd ~/Hiseq111005/Indx11/Indx11_cufflinks cd ~/Hiseq111005/Indx13/Indx13_cufflinks cd ~/Hiseq111005/Indx14/Indx14_cufflinks cd ~/Hiseq111005/Indx15/Indx15_cufflinks nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf accepted_hits.sam & * Genome-miner mkdir ~/RNAseq//Hiseq111005/Indx3/Indx3_cufflinks cd ~/RNAseq//Hiseq111005/Indx3/Indx3_cufflinks nohup samtools view -h ../Indx3_tophat-G/accepted_hits.bam > accepted_hits.sam & mkdir ~/RNAseq//Hiseq111005/Indx4/Indx4_cufflinks cd ~/RNAseq//Hiseq111005/Indx4/Indx4_cufflinks nohup samtools view -h ../Indx4_tophat-G/accepted_hits.bam > accepted_hits.sam & mkdir ~/RNAseq//Hiseq111005/Indx5/Indx5_cufflinks cd ~/RNAseq//Hiseq111005/Indx5/Indx5_cufflinks nohup samtools view -h ../Indx5_tophat-G/accepted_hits.bam > accepted_hits.sam & mkdir ~/RNAseq//Hiseq111005/Indx6/Indx6_cufflinks cd ~/RNAseq//Hiseq111005/Indx6/Indx6_cufflinks nohup samtools view -h ../Indx6_tophat-G/accepted_hits.bam > accepted_hits.sam & mkdir ~/RNAseq//Hiseq111005/Indx12/Indx12_cufflinks cd ~/RNAseq//Hiseq111005/Indx6/Indx6_cufflinks nohup samtools view -h ../Indx6_tophat-G/accepted_hits.bam > accepted_hits.sam & nohup ~/bin/cufflinks-1.1.0.Linux_x86_64/cufflinks -g ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf accepted_hits.sam & =====comparison of genes.fpkm_tracking===== * count cufflinks genes ID: cd ../Indx3_cufflinks/ cd ../Indx4_cufflinks/ cd ../Indx5_cufflinks/ cd ../Indx6_cufflinks/ cd ../Indx7_cufflinks/ cd ../Indx8_cufflinks/ cd ../Indx9_cufflinks/ cd ../Indx10_cufflinks/ cd ../Indx11_cufflinks/ cd ../Indx12_cufflinks/ cd ../Indx13_cufflinks/ cd ../Indx14_cufflinks/ cd ../Indx15_cufflinks/ awk '{print $5}' genes.fpkm_tracking | sort | uniq | wc -l > count_genes.fpkm_tracking less count_genes.fpkm_tracking * table There are no much difference in table organization or genes calling The only difference in gene numbers, I believe, is due to the latest gtf I downloaded in genome-minor which leads to more annotations. It actually means the matrix problem I met last time is not due to cufflinks files, but the script itself. {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''tophat w/o G''' | align="center" style="background:#f0f0f0;"|'''tophat w G''' | align="center" style="background:#f0f0f0;"|'''''' |- | cufflinks_Indx3||21266||21913||genome-miner |- | cufflinks_Indx4||21250||21896||genome-miner |- | cufflinks_Indx5||21238||21881||genome-miner |- | cufflinks_Indx6||21253||21896||genome-miner |- | cufflinks_Indx7||21348||21344||meangenemachine |- | cufflinks_Indx8||21210||21212||meangenemachine |- | cufflinks_Indx9||21198||21196||meangenemachine |- | cufflinks_Indx10||21209||21221||meangenemachine |- | cufflinks_Indx11||21200||21208||meangenemachine |- | cufflinks_Indx12||21155||21805||genome-miner |- | cufflinks_Indx13||21290||21292||meangenemachine |- | cufflinks_Indx14||21257||21255||meangenemachine |- | cufflinks_Indx15||21158||21159||meangenemachine |}
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