Entering edit mode
3.9 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!
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.
ok thanks for giving me the keywords to start searching. Will this require python?