Looking For Published Workflows Of Noncoding Rna Analysis

Question

[Honey]

Any one could suggest me a work flow published/ basic strategy to analyze differential level of noncoding RNA as well identification of novel noncoding RNA especially long noncoding ones. I have 100XPE Ribo-depleted data set.

Thanks

Answer 1

[Josh Herr]

You didn't give us much information on what your research question is or what organism you are studying. The workflows for small RNA identification can vary a lot depending on the question you are asking and the identification process is not trivial and often consists of many parts (i.e. looking for 21mers, 24mers, etc. etc.).

Check out this review article (Experimental approaches to identify non-coding RNAs) and this PhD dissertation (Bioinformatic identification of functional noncoding elements and expressed noncoding RNAs) on the topic for information on analysis pipelines. I have recently used both of these references to address an an analysis pipeline for sequencing of small RNAs for a novel plant genome.

[Honey]

It for hg19 I cannot access thesis, which may have been useful resource? Do you have access to this thesis?

[Josh Herr]

I was able to download and view through my university library. Are you associated with a university?

[Honey]

Yes I am however it is not allowing me to download the same do You mind sending as attachment or drop box or downloaded link to [e-mail] Thanks for your help

Answer 2

[biorepine]

You can refer to my answer may be How To Design A Long Noncoding Rna Detection And Quantification Experiment

[Honey]

Thanks. It apear to be too complex. Is thsi is the best way as You see below Chris is suggesting a work flow which is different from what you ar esaying. I dont want to favor one over another but with my limited knowledge trying to find what is best way to go. I want to find novel as well DE of known hg19 long noncoding RNAs from RNa seq Hi-seq PE data fro hg19.

Answer 3

[Chris Cabanski]

For identification of novel long noncoding RNAs, I would check out the following papers:

using TopHat + Cufflinks: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152676/

using TopHat + Cufflinks + Scripture: http://genesdev.cshlp.org/content/early/2011/09/02/gad.17446611.abstract

Once you have a set of noncoding RNAs that you're interested in (novel + existing), you should be able to use any standard RNA-seq differential analysis pipeline (CuffDiff, DESeq, edgeR, etc).