Question: RNA-Seq DEGenes Without GTF
gravatar for isu2017
9 months ago by
isu20170 wrote:

I am working a specific species where we have a reference genome, and I was able to align our RNA-seq data to it. However, I am looking to create a count table to funnel our dataset to edgeR for DE analysis. I don’t have a GTF to use with something like HTSeq. Anybody have an idea of how to proceed?

rna-seq • 310 views
ADD COMMENTlink modified 9 months ago by RamRS22k • written 9 months ago by isu20170

It's a species that has a reference genome but that is not well annotated in terms of gene expression? If that is the case, I would have done:

  1. HISAT2 / StringTie to produce a reference transcriptome GTF
  2. Use HTseq with the new GTF to derive raw counts
  3. Feed raw counts into EdgeR
ADD REPLYlink written 9 months ago by Kevin Blighe44k
  1. ...
  2. ...
  3. ...
  4. extract the unannotated gtf features and blast them to get an annotation.
ADD REPLYlink modified 8 months ago • written 8 months ago by h.mon26k

Valeu, cara!

ADD REPLYlink written 8 months ago by Kevin Blighe44k
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