Hi, I have .bam files aligned by hisat2 using genome FASTA file as the reference, after that I made up my mind to use SUPPA2 for the detection of Novel splice variants which recommends Salmon for transcript quantifications due to their TPM values, however, salmon uses the transcriptomic.fasta as a reference so my bam files would not be reliable with salmon. so it seems that I will rerun the alignment with another aligner like STAR to be compatible with salmon or use salmon itself from the beginning of the analysis with fastq files for TPM quantification.
Q1: Which is more accurate, use STAR as the aligner then use salmon, or use salmon from the beginning with fastq files?
Q2: Is it more accurate in detection of Novel splice events to align data against genomic reference instead of transcriptomic reference? If that right!.... Which aligner do you recommend?
I really appreciate your support. Thanks,