Checking sequence similarity between 2 RNAseq samples
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
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Triple Nipple •
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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.