Question: Does salmon use phred scores while pseudoaligning (and/or validating mapping)?
0
gravatar for Anthony
22 months ago by
Anthony0
Anthony0 wrote:

Dear Biostar Community,

I would like to know if salmon uses phred scores while pseudoaligning (and/or validating mapping)?

In the negative, what is the reason behind this the choice?

Thanks in advance,

Anthony.

phred salmon • 541 views
ADD COMMENTlink modified 20 months ago by karni_bedirian0 • written 22 months ago by Anthony0
2
gravatar for Rob
22 months ago by
Rob4.6k
United States
Rob4.6k wrote:

Hi Anthony,

No; salmon does not use the PHRED score, either while mapping or aligning. The main reason for not using it during alignment or mapping is that it just tends not to be very useful for this purpose. If a nucleotide inside a reasonably long exact match is bad quality (and therefore likely wrong), it’s almost certainly wrong in all of the mappings where it appears. In terms of finding the best locus (or loci) for the read, the quality score just turns out not to be very useful, while using it incurs extra processing cycles. Clearly, there _are_ cases where the quality scores are useful (e.g. in downstream variant detection, etc.) — however, we found them not to be helpful for our purposes and so we don’t use them.

Best, Rob

ADD COMMENTlink written 22 months ago by Rob4.6k
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