# DE lncRNA analysis pipeline
**URL:** https://help.galaxyproject.org/t/de-lncrna-analysis-pipeline/2260
**Category:** usegalaxy.org support
**Tags:** gtn-tutorial, troubleshooting
**Created:** [October 9, 2019, 6:36pm UTC](https://help.galaxyproject.org/t/de-lncrna-analysis-pipeline/2260 "2019-10-09T18:36:05Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Deniz](https://help.galaxyproject.org/u/Deniz)
#### Post date: [October 9, 2019, 6:36pm UTC](https://help.galaxyproject.org/t/de-lncrna-analysis-pipeline/2260/1 "2019-10-09T18:36:05Z")
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
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### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [October 11, 2019, 9:02pm UTC](https://help.galaxyproject.org/t/de-lncrna-analysis-pipeline/2260/2 "2019-10-11T21:02:18Z")
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](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> [Galaxy Training Network Tutorials](https://training.galaxyproject.org): Some [GTN](https://galaxyproject.org/teach/gtn/) tutorials are appropriate for [Galaxy Main](https://usegalaxy.org) 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](https://galaxyproject.org/use/) server choices. If a tutorial is supported by a pre-configured [Galaxy Docker](https://hub.docker.com/r/bgruening/galaxy-stable/) 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/:](https://galaxyproject.org/support/:)
- [Extended Help for Differential Expression Analysis Tools](https://galaxyproject.org/support/diff-expression/)