Any suggested work flows for lncRNA detection/prediction using RNA-Seq data?

04 April 2014 1 5K Report

I have RNA-Seq data for different cell lines and I'm looking to find lncRNAs which maybe deferentially expressed.

Hello!

Here is a really good 'step by step' for RNA-seq with R/Bioconductor (after alignment with (Bowtie2 or BWA) and compression and sortng with Samtools). You could go through the edgeR steps. This will get you a table of differentially expressed sequences then you can look for lncRNA specifically. Good Luck!

http://homer.salk.edu/homer/basicTutorial/rnaseqR.html

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