Hi all, I am trying to work with rMATS to analyse splicing events. With the new version of rMATS, they started using STAR and it does not allow using fastq's with different read length. My fastq read lengths vary between 41 to 50. Here is the link for one of my fastqc results, which actually represents the remaining 3 samples as well.. As seen in figure, there is a ~13 bp sequence that does not look ok. First question is, I believe that region is adapter seq., what do you think? Second question is, is it ok to manually trim the first 13 bps? I tried to trim according to phred scores but when I fastqc the phred-score-trimmed fastq files, nothing changed in figures. I need to figure out a way to equalize the read lengths... Any help would be very appreciated.
