I am trying to associate reads from a fastq file produced by a MiSeq run with the clusters listed in the .cif and .locs files from the run.
Unfortunately, the x and y locations extracted from read names in the fastq file do not appear to be the same as the x and y locations listed in the .locs files. By plotting all coordinate pairs from the .locs file for a tile and all coordinate pairs from all reads from that tile, it looks like fastq coordinates are produced from .locs coordinates by multiplying by around 10 and shifting some amount. Does anyone know exactly what this transformation is?
Unfortunately, the x and y locations extracted from read names in the fastq file do not appear to be the same as the x and y locations listed in the .locs files. By plotting all coordinate pairs from the .locs file for a tile and all coordinate pairs from all reads from that tile, it looks like fastq coordinates are produced from .locs coordinates by multiplying by around 10 and shifting some amount. Does anyone know exactly what this transformation is?