ncRNA incluidng lincRNA analysis

Question

[kanwarjag]

What is the best (options) for analyzing a Illumina Seq data for ncRNA including lincRNA. Is there a standard work flow?

Thanks

[Devon Ryan]

Depends on the organism. For human/mouse/etc. there are some OK annotations via lncRNAdb, Ensembl, etc. that you could start with.

[kanwarjag]

It is human I can use Broad database. I am more concerned about how I can reach at a final list of differential list of ncRNA.

[Manvendra Singh]

do you mean differential expression, or just the list which is detected in one but not in other ?

[kanwarjag]

Yes present in one samples.but not in other

[Manvendra Singh]

In this case , run the pipeline shown

http://www.biomedcentral.com/1471-2105/13/331/figure/F1

then see which transcript you find in one sample but not in others

Answer 1

[Manvendra Singh]

If you are looking for novel lncRNA, then here is nice pipeline , they use RABT assembly, and the cufcompare, and then they run lncRscan script on the outputs.

http://www.biomedcentral.com/1471-2105/13/331/figure/F1

from the study

http://www.biomedcentral.com/1471-2105/13/331

If not, then just map your reads, TopHat or STAR, then run cufflinks providing lncRNA or ncRNA GTF file (http://www.gencodegenes.org/releases/19.html)

then do some filtering, FPKM thresholds, or length thresholds.

HTH

Answer 2

[Chirag Nepal]

There are some methods paper.

However you could always start like

1. Map your reads to genome and do de-novo transcript assembly to identify novel ncRNA (small and long).
2. Do read counts to see which are (highly) expressed. Get differentially regulated genes.
3. Do analysis on genomic location, overlap coding genes, sequence conservation, secondary structure, syntenty conservation.
4. Check how many coding genes have processed small RNAs, in promoter, CDS and UTRs,
5. Check how the ends of ncRNAs are processed, look for some reads if they map in some particular way towards their 5'-3'-ends.

Answer 3

[f0e45afb]

Hi,

I wrote a similar pipeline which also categorizes lncRNAs into different classes. Take a look: http://git.io/SaFh1g