Identify reads that protein-coding and non coding (lncRNAs) for analysis long non coding RNAs

Question

[Saeed]

Dears

I would analysis lncRNAs data between conditions. I did DE analysis for coding protein using hisat2 - stringtie and Deseq2. Now I want to do DE for long non coding reads (more than 200 nt).

Really appreciate your help and guidelines. Thank you in advance.

Answer 1

[Prash]

Dear Saeed Assuming that these ar eall humans, the DElncRNAs could be batch downloaded from Entrez or ensembl Biomart and blasted against NONCODE.org darabase V6/animal/human) and the best hits could be considered as lncRNAs

Nevertheless, the candidate lncRNAs and other DEGs could be developed first with PCA plots and followed by heatmaps. Many lncRNAs are upregulated and you could check for their coding potential if any of them are interesting and to be validated using downstream approaches using qPCR

Regards prash

Answer 2

[Saeed]

Dear Prash, Thank you very much for your good explanation. But still I need more detail to understand the workflow as it seems to me the analysis of DE lnonRNA is not stiaght way as coding genes for example algiment, assembly, quantitificaton and finally enrichment analysis. Is there any detailed documents on how do it?