I would like to analyze fastQ files from MiSeq Illumina. For this I want to do a DNA alignment on a reference genome and then a polymorphism detection at known positions (bed file).
The problem is that the sequencing was done with UMIs, for low-intensity polymorphism detection. I don’t know what tools to use to do the alignment taking into account the UMIs (if possible).
So I have 4 fastQ files, R1 and R2 because double end sequencing and I1 and I2 which contain the indexs and UMIs sequences (I1 = index I7 + UMI and I2 = index I5).