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Posted by colin on Fri 01 of Aug., 2008 09:01 MYT

Novoalign parameters for reporting multiple alignments to each read.

Posted by colin on Fri 01 of Aug., 2008 09:01 MYT

Hi,
We are having a debate on which NovoAlign parameters are
more appropriate.
If you guys have a quick second, can you comment on the
differences between the two parameter choices below?

novoalign -R 130 -r Exhaustive -t 130 -d Celegans.novo -q $_

novoalign -R 30 -r All -t 130 -d CElegans.novo -q $_"

Posted by colin on Fri 01 of Aug., 2008 09:03 MYT

Posted by colin on Fri 01 of Aug., 2008 09:03 MYT

Hi,

It depends a bit on what you're looking for. I'll try to explain parameters and how it might affect your choice.

First, the search is usually iterative so we look for a perfect match and keep adding 30 to the threshold until we find a match or reach the threshold limit specified by the -t option.

The -R 30 option says to extend the search at least 30 points further than the best match so it should find the best alignment and any alignments within a score of 30 of the best. -r All will then print all these alignments. So if the best alignment scores 0 you will get reported all (there are some heuristics once you pass the best alignment so it might not be all) alignments with score between 0 & 30. Similarly if best alignment scored 20 then all alignments with a score from 20 to 50 would be reported.

The -r E option turns off iteration and search will look for all alignments with a score below the -t threshold.