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Old 04-14-2015, 12:05 AM   #1
xunong
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Default How to identify known lncRNA from RNA-seq data?

Hi guys,

As I have some RNA-seq data, and have already run the TopHat-cufflinks to get the transcripts.gtf file, then how do I identify the already annotated lncRNAs from the gtf file?
Besides, I've two groups of data, one is control and the other one is gene knock down group, can I perform DE analysis of lncRNAs after identified them?

I'm new to lncRNAs, do u guys have any suggestions?
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Old 04-14-2015, 07:25 AM   #2
cascoamarillo
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I'm also interested into this kind of lncRNA analysis. Check out this recent paper:
http://biorxiv.org/content/biorxiv/e...17889.full.pdf


Quote:
Originally Posted by xunong View Post
then how do I identify the already annotated lncRNAs from the gtf file?
So, are they already annotated?
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Old 04-14-2015, 05:49 PM   #3
xunong
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Well, I downloaded a bed file of known LncRNA from Noncode databasehttp://www.bioinfo.org/noncode/index.php, for my gtf file, can I just pick up ones that have overlap with this bed file according to chr start/end site?
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Old 11-18-2015, 07:55 AM   #4
kongantik
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Xunong,

I wrote a pipeline that does what you are looking for.

http://git.io/SaFh1g
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Old 04-16-2017, 01:47 AM   #5
shakilvet
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is it possible to identify lncRNA from RNA SEQ data. As the data consists of only cDNA molecules which are synthesised from mRNA
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Old 04-17-2017, 10:16 AM   #6
kongantik
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Quote:
Originally Posted by shakilvet View Post
is it possible to identify lncRNA from RNA SEQ data. As the data consists of only cDNA molecules which are synthesised from mRNA
If you do Total RNA sequencing at high depth, you will able able to identify ncRNA. If you do mRNA-Seq, then no. Illumina provides kits for Total RNA-seq for Human, Mouse and Rat, wherein you can remove rRNA and then sequence rest of the RNA.
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