Question: Filtering lncRNAs from total RNA
0
gravatar for aropri
3 months ago by
aropri10
aropri10 wrote:

I am trying to analyze data from patient samples. I took the data of RNA seq from this paper: https://www.mdpi.com/2075-4426/9/2/18/htm

I want to look at specifically lncRNAs and how they change from normal to cancer cells. I have done alignment using STAR and ran DEseq2 for differential expression on total RNA. I was wondering if there is a way to filter out only lncRNAs and look at differential expression for those. Any help is appreciated.

rna-seq • 146 views
ADD COMMENTlink written 3 months ago by aropri10
  1. download the Gencode annotation https://www.gencodegenes.org/

  2. Get the respective biotypes of all the genes https://www.gencodegenes.org/pages/biotypes.html

  3. and filter according to the biotypes you need. You may need to run the DESeq again on the filtered set only

ADD REPLYlink written 3 months ago by Santosh Anand5.2k
1

lncRNA GTF file is available separately at GENCODE. No need to separate out biotypes.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax92k

How do I use the lncRNA gtf file to filter out the lncRNAs from the total RNA that I have aligned using STAR. Hope you can provide a little detail. I am new to RNA seq so any help is appreciated.

ADD REPLYlink written 3 months ago by aropri10
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