DE lncRNA analysis pipeline

[Deniz]

Hi,
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.

Best,

Deniz

[jennaj]

Hi,

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

Troubleshooting resources for errors or unexpected results

Galaxy Training Network Tutorials: Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

If you run into any problems, this FAQ summarizes the most common reasons with solutions/link outs to other FAQs https://galaxyproject.org/support/:

• Extended Help for Differential Expression Analysis Tools