Rui:Matrix

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Matrix[edit]

  • Modify Dr. Zhang's script by replacing folder names (such as “tophat_Mm_Indx3” -> “Indx3_cufflinks)
  • Under cufflinks_UCSC folder, nano and paste modified script in, save "Combine_geneTracking.pl" (automatically save as -rw-r--r-- in current directory)
  • Executive: chmod 755 Combine_geneTracking.pl
  • Run: ./Combine_geneTracking.pl > gene_expression_matrix.txt
Problem: I ran tophat w/o G correction, so that output of cufflinks (genes.FPKM_tracking) has no gene annotation. Have to repeat tophat with G correction