long non coding RNA

Question

[HK]

Hey everyone..

I have the sample having total transcriptome using Ovation® RNA-Seq System V2. So, i am doing the analysis now. The pipeline i am using is fastQC--> trimmomatic --> tophta2 (using USCS hg19) but now trying GENCODE also as it has the better annotation for log non coding RNA --> featurecounts (quantification).

Do you recommend the same , so should i try using any other tools.

CAn i also find circular RNA from my samples?

Answer 1

[igor]

GENCODE has many lncRNAs annotated. You also should look into MiTranscriptome (large-scale ab initio transcriptome meta-assembly from 6,503 RNA-Seq libraries): http://mitranscriptome.org/

I don't know much about circular RNAs. I believe you have to check for divergent read pairs after alignment. Not sure if there are any specialized tools that exist.

[HK]

Thanks.. i will look into mitranscriptime

Answer 2

[fanli.gcb]

See this thread: Detect circular RNA using RNA-seq

I've found CIRCexplorer to be reasonably easy to use with tophat: https://github.com/YangLab/CIRCexplorer2

Recent review: http://www.nature.com/nrg/journal/v17/n11/full/nrg.2016.114.html

[igor]

CIRCexplorer looks really nice. Supports multiple aligners, excellent documentation, actively developed.