I am thinking about using the KisSplice workflow to call SNPs between 2 closely related species. I have a Trinity assembly, and a transdecoder ORF file.
I have 4 paired-end samples total for 2 species - 2 samples per species. I would like to call SNPs between species 1 and species 2, to highlight the functional differences between these species.
According to this: kissplice -s 1 -k 41 --experimental -r cond1_replicat1_R1.fastq -r cond1_replicat1_R2.fastq -r cond1_replicat2_R1.fastq -r cond1_replicat2_R2.fastq -r cond2_replicat1_R1.fastq -r cond2_replicat1_R2.fastq -r cond2_replicat2_R1.fastq -r cond2_replicat2_R2.fastq
Would the SNPs that KisSplice calls be between cond1 and cond2 only? Or would it call SNPs between all combinations of cond1, replicate 1, replicate 2, cond2, replicate 1, replicate 2 etc?
My goal is to observe the number of SNPs that makes species 1 different from species 2, and which of those SNPs would cause an amino acid change.
Please let me know if this workflow is appropriate for my objective. Thank you.