Rui:Matrix 10.30.11

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Matrix 10.30.11[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