Question: RNA-Seq DEGenes Without GTF
0
gravatar for isu2017
12 weeks ago by
isu20170
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 • 172 views
ADD COMMENTlink modified 12 weeks ago by RamRS19k • written 12 weeks ago by isu20170
2

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 12 weeks ago by Kevin Blighe33k
1
  1. ...
  2. ...
  3. ...
  4. extract the unannotated gtf features and blast them to get an annotation.
ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by h.mon22k

Valeu, cara!

ADD REPLYlink written 12 weeks ago by Kevin Blighe33k
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