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Old 09-21-2012, 12:30 AM   #1
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Join Date: Sep 2011
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Default identical results from different normalization methods in cuffdiff v2.0.2?

version: cuffdiff v2.0.2,
two normalization methods are used, including compatible-hits-norm and total-hits-norm. however, the file of isoform_exp.diff are identical, I want to know why?

cuffdiff -o -p 8 --total-hits-norm -L R1,R2,R3 -u./UCSC.hg19.gtf ./R1/accepted_hits.bam ./R2/accepted_hits.bam./R3/accepted_hits.bam
#2. --compatible-hits-norm
/cuffdiff -o diff_out.ucsc.compatible-hits-norm -p 8 --compatible-hits-norm -L R1,R2,R3-u ./UCSC.hg19.gtf ./R1/accepted_hits.bam ./R2/accepted_hits.bam ./R3/accepted_hits.bam
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