lncRNA identification from RNAseq data

Question

[pipe_cvm2]

Hello,

I have some Zea mays rna data that I have analised for Differentially expressed genes, aligned with HISAT2,stingtie etc

Now I am interested in identifiying lncRNA sequences out of all the transcripts aligned. My data was polyA enriched, so it´ll be biased but I think it might be interesting to see the result.

Any tips on how to extract the lncRNA out of all the transcripts aligned? I believe that with stringtie files and gffcompare would be possible to extract the lncRNAs but I´m not sure where to start.

Any help is appreciated. Many thanks, Felipe

[ATpoint]

Do you want to identify novel non-coding RNAs or just pull out the lncs form existing annotations, so basically a GTF file?

Answer 1

[EagleEye]

A: Any One please provide protocol for Analysing long noncoding RNA illumina NGS da