RNA-Seq DEGenes Without GTF

0

Entering edit mode

5.6 years ago

isu2017 • 0

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 • 1.2k views

ADD COMMENT • link updated 5.6 years ago by Ram 43k • written 5.6 years ago by isu2017 • 0

2

Entering edit mode

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:

HISAT2 / StringTie to produce a reference transcriptome GTF
Use HTseq with the new GTF to derive raw counts
Feed raw counts into EdgeR

ADD REPLY • link 5.6 years ago by Kevin Blighe 87k

1

Entering edit mode

...
...
...
extract the unannotated gtf features and blast them to get an annotation.

ADD REPLY • link 5.6 years ago by h.mon 35k

0

Entering edit mode

Valeu, cara!

ADD REPLY • link 5.6 years ago by Kevin Blighe 87k

Login before adding your answer.