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ngsfilter: pattern matching
#1
What is the general structure of the pattern match that ngsfilter searches for?

If this is the format of my sequences $tag1$fprimer.*$rprimer$tag2  where
$tag1 is the first tag in the sample description file
$fprimer is the forward primer
.* is posix regex, meaning 1 to any number of bases of any identity
then it seems to work fine.

What if, for some reason, there are extra bases in front of the tag1, will ngs filter still recognize a match or does it require that the tag be at the beginning of the line?

Will ngs filter also detect the following patterns?    

$fprimer$tag1.*$rprimer
$tag1$fprimer.*$rprimer

I have some data that is formatted like this, and need to demultiplex it.
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#2
HI Cbird,

yes the general format is $tag1$fprimer.*$rprimer$tag2

The tag have not to at the begining of the sequence but sticked at the 5’ end of the primer.

therefore this pattern $fprimer$tag1.*$rprimer cannot be recognized
but this one yes : $tag1$fprimer.*$rprimer just use dash - for the missing tag in the ngsfilter file

Eric
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#3
That's helpful, thank you!

I suppose the tag could be listed as a primer and the primer as a tag for $primer$tag demultiplexing
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#4
Tags are usually short and non discriminant. The algorithm looks for primers with a free end gap alignment algorithm, and considers the bases at the 5’ end of the primer match as the tag without any mismatches. So no you cannot just invert tags and primers
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#5
roger that, thank you!
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