Entering edit mode
12 weeks ago
ZZOYEA
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20
Hello, I am currently using the Tuxedo pipeline to identify lncRNAs. I obtained transcript assemblies for each sample using cufflinks, combined them into a single file with cuffcompare, and then extracted lncRNAs based on the class code.
My question is about how to proceed with differential analysis after obtaining the lncRNAs. I intended to create a reference using the combined assembly file produced by cuffcompare and then perform RSEM based on that reference. However, I noticed that when I check the results from RSEM, a single gene is split into multiple parts, and the count values are measured separately.(As you can see in the image below) Do you know why this might be happening?
- Is it incorrect to create a reference using the cuffcompare result? I'm concerned that if a single gene is split into multiple parts like this, it may pose difficulties in obtaining differentially expressed genes.
- Are there other good methods for using RSEM after cuffcompare to measure lncRNA expression?
- Or, are there other effective methods for determining the expression levels of each lncRNA?
