Any recommendation for novel lncRNA pipelines from RNAseq data?

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6.7 years ago

Daisy ▴ 60

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

lncRNA • 2.5k views

ADD COMMENT • link updated 6.6 years ago by Biostar 20 • written 6.7 years ago by Daisy ▴ 60

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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

ADD REPLY • link 6.7 years ago by Kevin Blighe 88k

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

ADD REPLY • link 6.7 years ago by Daisy ▴ 60

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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.

ADD REPLY • link 6.6 years ago by ATpoint 86k

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