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Old 12-01-2014, 12:58 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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1. I'd use IGV and make either a BED or GTF file describing the lncRNA locations in the scaffold. If you add your gene of interest to it too then you can easily visualize where things are relative to each other (you can also do this in R with packages like Gviz, but I think just using IGV will be a bit easier for your needs).
2. RNAcentral has the lncRNA sequences from Ensembl and lincRNAdb, so have a look at it. It's interface isn't great at the moment, so you'll have to download and parse the fasta file (I actually have some tools to do this that I need to post on github).
3. No clue, hopefully someone else knows.

Last edited by dpryan; 12-01-2014 at 01:02 AM.
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