Where to get read sequences and qualities?
I only know a bit about SolexaPipeline. So far as I know, read sequences can be acquired from Bustard, after Gerald filter or after Gerald quality calibration. I usually recommend to get the data after quality calibration because both sequences and qualities are most accurate there. Nonetheless, if you feel it difficult to get calibrated qualities, you may also use the data filtered in Gerald. My opinion is not to use unfiltered data. Do not be lured by the amount of data you get before filter. These data mostly bring troubles instead of a better result. • Longer reads or better qualities, what do you prefer? I prefer better qualities. Longer reads may seem attractive, but if you cannot get very high-quality data at 3′-end of reads, you should definitely stop sequencing or trim off the low-quality ends of all reads. Although maq is still sensitive enough to align reads with very poor tail, the errors in these reads may be highly dependent and somewhat weird, which may cheat maq into ca
