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Old 03-20-2014, 06:16 AM   #9
sprocha
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Location: spain

Join Date: Mar 2014
Posts: 2
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right... I am only using those "illuminaclip" instructions (to trim the primers)... nothing else.. but thanks for the grep suggestion - I will confirm these.

Also, an additional question: trimm (and others I guess) are fw and rev sets of both paired and unpaired reads.

Am I correct of assuming that I should use both paired and unpaired reads for te assembly? (unpaired being reads where only one was kept, pair being dropped)... because it seems to be that some people usually discards the "unpaired" files. I can see why, being few data... and most likely many "borderline" to being discarded... so not very informative... but it has not necessarily to be like that, right? One should use these unpaired as well, or not??

many thanks in advance again,
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