Hi Guys,
I've been trying to use either Ssaha or Smalt to align both Illumina and 454 reads (not at the same time, of course!). I wanted to output SAM format. But I'm not sure if the quality scores will be encoded correctly...
I can't find anywhere in the manual that says which version of Fastq these programs want. I understand Fastq can be either ascii+33 or ascii+64. To the best of my knowlegde, neither Ssaha or Smalt use quality score information during alignment, however if it is output in the Sam format, then surely how it interprets the Fastq quality encoding will have an impact on how it is output in SAM? (which I think is always ascii+33?).
If anyone can shed any light on this problem I'd be most grateful...
Kerensa.
I've been trying to use either Ssaha or Smalt to align both Illumina and 454 reads (not at the same time, of course!). I wanted to output SAM format. But I'm not sure if the quality scores will be encoded correctly...
I can't find anywhere in the manual that says which version of Fastq these programs want. I understand Fastq can be either ascii+33 or ascii+64. To the best of my knowlegde, neither Ssaha or Smalt use quality score information during alignment, however if it is output in the Sam format, then surely how it interprets the Fastq quality encoding will have an impact on how it is output in SAM? (which I think is always ascii+33?).
If anyone can shed any light on this problem I'd be most grateful...
Kerensa.