Hello. I am currently conducting an analysis to identify lncRNAs from total RNA-seq data. I have a couple of questions.
I have tried both the Cufflinks-Cuffmerge-Cuffcompare pipeline and the StringTie-gffcompare pipeline. However, the results from each pipeline are quite different.
The StringTie pipeline was significantly faster, but the Cufflinks pipeline yielded a higher total number of lncRNAs. Additionally, some transcripts were present only in the results from the StringTie pipeline, while others were found only in the Cufflinks pipeline. There were very few overlapping transcripts between the two.
In this situation, which pipeline's results can I trust more? Since the results are different, I am unsure which one to believe. Alternatively, would it be acceptable for me to combine the results from both pipelines?
