Can I assemble 1 chromosome only with RNA-Star -- Custom Genome, Variant calling, RNA-seq

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Hi,
I want to call a variant from a gene on a publicly available data set.
These are transgenic mice expressing a human transgene not present in rodents.

My plan is to map the read to a human reference genome using STAR and then call variants with FreeBayes. My question is if instead of using a whole reference genome, I can only use Chromosome 22 which is where the gene is.

Is that possible?
Thanks!

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Hello @AgustinGV

I’m not exactly sure what you are trying to do but that you can explain more if needed.

STAR will not create a reference assembly.

You can use an existing assembly from your target genome, in whole or in part, as a Custom Genome/Transcriptome to call variants that exist in the RNA-seq dataset. You can also assemble a reference transcriptome.

That said, I would suggest reviewing the publication related to the work you are trying to replicate – what reference did they use? It should be the same in your work or expect different results/statistics.

Please see this related prior Q&A for more options. The tutorials under “Variant Analysis” would also probably apply for your case. Galaxy tools for the de novo assembled transcriptome annotation

Thanks!

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Thanks for the answer, my previous post was unclear. I rewrote it for clarity.
From your answer though I think that what I want to do is called a “custom genome”. I am exploring the tool NormalizeFASTA from the link.

Thank you!

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