Question: Any Thing Wrong With My Cufflink Process In Galaxy?
6.4 years ago by
yao chen • 50
yao chen • 50 wrote:
Dear all: Recently, I run cufflink in galaxy on the internet. I want to compare two samples, However, I found no transcript or gene passed the significant level, even many of them have large FPKM in one sample and 0 FPKM in another sample. Any thoughts? Below is my cufflink process: I have four samples belong to two group. the test have three samples, and the control has one sample. First, using accept_hit.bam from tophat, I run cufflink without annotation on each sample. Then, for the four "gtf" files from four samples, I run cuffcompare to combine these transcript and compare to the annotation genome. However, at this step, I found the transcript accuracy is very low. See one example: Missed exons: 10673/11776 ( 90.6%) Wrong exons: 1254/2007 ( 62.5%) Missed introns: 8529/8637 ( 98.7%) Wrong introns: 2/5 ( 40.0%) Missed loci: 0/504 ( 0.0%) Wrong loci: 1248/2002 ( 62.3%) at last, I run cufdiff between this two group sample. Thank you.
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