Any recommendation for novel lncRNA pipelines from RNAseq data?

Question

[Daisy]

hello guys

Do you have any recommendations for finding novel lncRNA from RNAseq data? I found this, but wanna look for you recommendations before spending time trying it?

https://www.nature.com/articles/s41598-017-14595-3

Thanks

[Kevin Blighe]

I do not see anything 'wrong' with using that pipeline. Scientific Reports is at the 'end of the line' in terms of the Nature Publishing Group's journals but that should not diminish the quality of research articles published there. I think that the majority of people would recommend HISAT2 and StringTie for general purpose of identifying novel RNA species - both of these are mentioned in the manuscript to which you have linked.

Kevin

[Daisy]

thank you. I am very new and walking on eggshells in bioinformatics :)

[ATpoint]

Given that you are not an expert in this topic, I recommend sticking with well-documented pipelines and tools that are being actively maintained. I do not know the tool in this link, but you should check if people cited it in primary publications (not reviews) and if you can get some helpful information from the methods sections of these papers. If not, better stick with HISAT2/Stringtie, as it is used by a wider community, means you can get more help.