DE lncRNA analysis pipeline

I am trying to identify differentially expressed lncRNAs in tumor samples (18 replicates) compared to control samples (3 replicates). The same library prep kit is used for all samples; however, 10 samples have 100 bp paired-end reads and others 150 bp pe reads.

I am planning to use Cutadapt tool to trim the 150 bp reads to 100 bp. And after trimming, I am planning to use "Tophat>Cufflinks (with Gencode lncRNA annotation>Cuffmerge>Cuffdiff " pipeline.

I know that Cufflinks tool is deprecated. I’d like to improve my pipeline. Any suggestion will be appreciated.



1 Like


Updated tutorials for DE analysis can be found here under the “Transcriptomics” section. These avoid using Tophat and Cuffdiff, too (are also considered deprecated).

If you run into any problems, this FAQ summarizes the most common reasons with solutions/link outs to other FAQs