I am working on alternative splicing. I have paired-end sequencing data of different length (100 bp for the forward and 66 for the reverse, trimmed because of low quality). My problem is that some tools for alternative splicing, such as MISO or rMATS, require reads of the same length. I could trim the reads to get the same size, and use both forward and reverse, but in this case all the reads will be quite short (66 bp). Alternatively I can use only the forward reads, which are considerably longer (100 bp). I searched a bit but I could not find a clear answer on which strategy would be better. To my knowledge is better to not use <70 bp reads for alternative splicing detection, but I find papers that publish alternative splicing data with 50bp reads single ends.
Any advice would be highly appreciated.