[sparks]

Hi korifuenc7933,

If you'd like to align using prb files Novoalign supports this. It usually improves alignment yield vs fastq files.
Colin

[Menato]

I heard about .prb. Nice information, i guess i should use it instead oj the fastq

[sparks]

One issue with prb files is that the prb values aren't calibrated against mismatch rates. I haven't seen any study to see if this is really a problem and how it might impact alignment and SNV calling.
It would be interesting if someone could look at concordance of SNP/Indel calls for an RNA dataset using prb, fastq & calibrated fastq. Another interesting project would be to look at calibrating prb probabilities.