This is a test version of Biostars. For the public version, visit https://www.biostars.org.
SNPs in 3UTR

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
• 921 views • link
written by ntsopoul 6

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.

• 0 views • link
written by ATpoint 9.1K

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

• 0 views • link
written by ntsopoul 6

0 answers

No answers yet.

Log in to answer this question.

More posts like this