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Question: Reference genome can it be partial?
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gravatar for RACHAMPION
20 months ago by
RACHAMPION • 10
RACHAMPION • 10 wrote:

I'm doing an RNA-seq on wheat to get differential expression of wild type vs a mutant. I'm only looking at a few specific genes. The wheat genome has not been fully sequenced, and for this problem it does not need to be. NCBI lists transcriptomes only. Can I use a program (e.g. Tuxedo suite) that requires a reference (in this case, the transcriptome) to do the differential expression? I would prefer the reference genome approach because it is simpler than deNovo assembly.

Thanks
assembly tophat alignment rna-seq • 583 views
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modified 20 months ago by shengweima • 0 • written 20 months ago by RACHAMPION • 10
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gravatar for Jennifer Hillman Jackson
20 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, these tools can be used with a transcriptome instead of a genome.

Use the Custom Reference genome feature with tools. It doesn't matter if the CG is partial. A CG is simply a fasta data in your history cleaned up with the tool NormalizeFasta using the options to wrap at 80 bases and to trim the title line at the first whitespace.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for shengweima
20 months ago by
shengweima • 0
shengweima • 0 wrote:

The wheat reference genome v1.0 has released. https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies I have used this reference in my rna_seq data.
ADD COMMENT • link written 20 months ago by shengweima • 0
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