splicing.dff from Cuffdiff
My workflow is tophat -> cufflinks ->cuffmerge-> cuffmerge, and I hoped to know the promoter usage and splicing events information through cuffdiff. The code for cuffdiff is
cuffdiff -p 12 -o ./KOTAC/ ./asm/merged.gtf -b ../genome.fa KO_1.bam,KO_2.bam,KO_3.bam,KO_4.bam WT_1.bam,WT_2.bam,WT3.bam,WT4.bam
But the output is kind of weird to me, the test statics in all lines of promoter.diff and splicing.dff are zero with NOTEST and LOWDATA. However, the gene_exp.diff looks reasonable. This guy has a similar problem http://seqanswers.com/forums/showthread.php?t=30197 , but he only has one replicate so that cuffdiff won't do the test. Here I have four replicates for each condition, but the cuffdiff still didn't do the test. Anyone can help me, thanks in advance!
cuffdiff -p 12 -o ./KOTAC/ ./asm/merged.gtf -b ../genome.fa KO_1.bam,KO_2.bam,KO_3.bam,KO_4.bam WT_1.bam,WT_2.bam,WT3.bam,WT4.bam
But the output is kind of weird to me, the test statics in all lines of promoter.diff and splicing.dff are zero with NOTEST and LOWDATA. However, the gene_exp.diff looks reasonable. This guy has a similar problem http://seqanswers.com/forums/showthread.php?t=30197 , but he only has one replicate so that cuffdiff won't do the test. Here I have four replicates for each condition, but the cuffdiff still didn't do the test. Anyone can help me, thanks in advance!