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 |