Question: RNA-Seq DEGenes Without GTF
gravatar for isu2017
23 days 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 • 126 views
ADD COMMENTlink modified 23 days ago by RamRS18k • written 23 days 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 23 days ago by Kevin Blighe30k
  1. ...
  2. ...
  3. ...
  4. extract the unannotated gtf features and blast them to get an annotation.
ADD REPLYlink modified 21 days ago • written 21 days ago by h.mon20k

Valeu, cara!

ADD REPLYlink written 21 days ago by Kevin Blighe30k
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