Aligning Human probe gene sequences against Pig reference genome using STAR

[pradeepbkarma]

Dear All!
I am trying to align human probe sequences from 10x genomics against the reference Pig reference genome to see if there is a 100% sequence match of human genes with the pig genes and if they have the homology in gene sequences. To perform this alignment, I have some confusion listed below:

1. Can I use the whole reference genome, and annotation GTF file in STAR index or should I use the transcriptome mRNA file?
2. Does STAR find the 100% sequence match?

[alexdobin]

Hi @pradeepbkarma

Can I use the whole reference genome, and annotation GTF file in STAR index or should I use the transcriptome mRNA file?
Both approaches should work. Since the probes are likely taken from the spliced transcript sequences, mapping to the transcriptome will be more sensitive.

Does STAR find the 100% sequence match?

Yes