Checking sequence similarity between 2 RNAseq samples

Question

[Triple Nipple]

Hi all

I have 2 RNAseq .bam files of two mouse samples, and I want to check the homology and similarity of the 3UTR sequences between them. Is there a way of doing this and getting a similarity score?

I would really appreciate any help!!

Thank you, TrpNip

[GenoMax]

I want to check the homology and similarity of the 3UTR sequences between them.

This is a bit of an odd request. Are these BAM files aligned to the same reference? If so you could simply try and create a consensus sequence for the regions you are interested in for the two files and compare them. Use this more as a qualitative assay.

Note: Unless the sequences are homologous they would not align in the region in the first place.