Variant calling from RNASeq

Question

[ifudontmind_plzz]

I would like to know if it is possible to do variant calling using single end RNAseq.

[ifudontmind_plzz]

@Kevin, thank you. I was wondering using single end RNA sequencing, how efficient it will be handling splice junctions.

[Kevin Blighe]

I have no frame of reference for that. However, if your intention is actually to identify splice-junctions, then there is likely some program already produced for this that can take single-end reads. A quick search leads me to this, what seems to be a review of some sort: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0697-y

Answer 1

[Kevin Blighe]

Yes, it is possible, but please consider the limitations: A: Inferring genotype based on RNA sequnces

Note also that Broad institute eventually removed the page to which I linked in my answer.

Kevin

[ifudontmind_plzz]

@Kevin, thank you. I was wondering using single end RNA sequencing, how efficient it will be handling splice junctions.