I am using tuxedo pipeline to analyse differential gene expression between my samples. I have 3 biological replicates from each group and 4 groups. Two groups are wild type whereas the other two groups are from knock out cells. However I am seeing this bizarre output where I am getting hits for the silenced gene in the knock out groups.
These are 100bp paired end reads from Illumina and I have done Trimmomatic to remove adaptor sequences, TopHat, Cufflink, Cuffmerge of all the Cuff link output files and Cuff diff.
I am clueless on what to do, could someone please help me? Any comments/suggestions welcome.