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Old 01-02-2015, 09:24 PM   #7
angel-sakura
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Location: Aus

Join Date: Nov 2014
Posts: 23
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Quote:
Originally Posted by docnj View Post
Hi angel-sakura, You said that you have extracted all predicted lncRNAs that close to the target genes by using PLEK. I'm confronted with the same problem myself, too. I have one interested target gene, but don't know how to find lncRNAs close to it. May I ask how you conducted the prediction through using PLEK? If you can also provide procedures in details, that would be appreciated very much!! Thank you!
Hi, sorry for the late reply, I was on holidays.
Check this link:http://sourceforge.net/projects/plek/files/
You can downloand the PLEK and its manual from above link. The PLEK is straight forward, you just input the fasta file, then it will produce an output containing coding and non-coding genes.
As for finding lncRNAs close to your gene of interet. The steps are: 1. extract the upstream and downstream sequences (such as 500kb) of your target gene. 2. Blast RNAseq data to fragment extracted from step 1. 3. predict the blast result with PLEK.

Cheers
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