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

I am trying to analyze data from patient samples. I took the data of RNA seq from this paper:

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

  2. Get the respective biotypes of all the genes

  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

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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