RNA-Seq DEGenes Without GTF

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6.8 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 • 1.4k views

ADD COMMENT • link updated 6.8 years ago by Ram 45k • written 6.8 years ago by isu2017 • 0

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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 6.8 years ago by Kevin Blighe 89k

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

ADD REPLY • link 6.8 years ago by h.mon 35k

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Valeu, cara!

ADD REPLY • link 6.8 years ago by Kevin Blighe 89k

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