Rui:Cufflinks 10.28.11

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cufflinks 10.28.11[edit]

  • 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[edit]
  • 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.
' tophat w/o G tophat w G '
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