SNPs in 3UTR

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4.0 years ago

ntsopoul ▴ 60

Hi,

I have RNA-seq (Tru-Seq) data from two conditions and I would like to compare the 3'-UTRs of the two transcriptomes regarding SNPs. I have no idea how to start... How do I extract only reads that mapped to the 3'-UTR and how do I compare the two conditions for SNPs? So far I have performed only DGE but no mutation or SNPs analysis. I would be glad if you could give me a rough plan I can follow.

Thanks a lot!

SNP RNA-Seq sequencing • 531 views

ADD COMMENT • link 4.0 years ago by ntsopoul ▴ 60

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Please use the search function. There are multiple of threads on how to extract UTR coordinates and how to perform variant calling from RNA-seq data. GATK has some best practices for variant calling from RNA-seq. RNA-seq is not the best assay to call variants from due to potential noise rom reverse transcription so be sure to validate results properly.

ADD REPLY • link 4.0 years ago by ATpoint 82k

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ok thanks for giving me the keywords to start searching. Will this require python?

ADD REPLY • link 4.0 years ago by ntsopoul ▴ 60

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