I looked at the forum but I couldn't find any answer to my question.
Since I don't have access to my actual dataset right now, I installed and tried test data to look for SNPs however results_reads1_reads2_k41_coherents_type_0a.fa or results_reads1_reads2_k41_coherents_type_0b.fa files are empty, It only gives output for Alternative Splicing events which is stored in results_reads1_reads2_k41_coherents_type_1.fa.
I used -s switch with either 1 or 2 but it still does not give me any results for SNP. Since I am new to SNP calling, I'm sorry if I'm asking something silly.
Thanks in advance! WM