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Old 04-30-2011, 10:14 PM   #1
Junior Member
Location: Beijng, China

Join Date: Apr 2011
Posts: 9
Default my understanding for cuffdiff output

Hi. I am a newbie in RNA-Seq analysis and now I am doing the pipeline with several software. I want to use cufflinks ,cuffcompare and cuffdiff to get DE genes,alternative splicing and novel transcripts and now I am confused about the output files cuffdiff gave me and I don't know what to do next. so the queston is:
1 Attached is a image I made to try to figure out the relationship of each file
I got from cuffdiff. But I don't know if it's right. so any advice will be
2 If I'm going to analysis the DE,should I get the gene list and do subsequent
analysis like GO enrichment?
If I'm going to analysis alternative splicing difference between the samples.
How should I proceed? statistics the number of AS events, make a
histogram or something?
If I'm going to analysis the novel transcripts ,what am I supposed to do?
Thank you in advance for your advice.
Attached Files
File Type: pdf cuffdiff_output_understanding.pdf (89.6 KB, 386 views)
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