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aligning RNA seq data against human genome

Hello,

I have some RNA-seq samples from different patients and I want to align them against human genome. I have two questions, 1) since my data is rna-seq should I align them against RNA genome? 2) I found this repository hg38 of human genome. As I read it is dna genome. So the answer is somehow dependent to the first question. Is it appropriate for my purpose? if RNA should be used which repository I can take?

variant calling rna-seq alignment

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updated 3.9 years ago by GenoMax

• written 3.9 years ago by Nemo •

1 answer

RNA data is generally aligned against the full genome reference. If you intend to call variants, as the tag suggests, then you should do that. Be sure to use an aligner that is splice aware (e.g. STAR, BBMap).

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written 3.9 years ago by GenoMax

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