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Old 10-14-2010, 03:40 AM   #3
nicolallias
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Location: France

Join Date: Jan 2010
Posts: 23
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Hi flxlex,
I'm considering de novo assemblies only, these observations are based on the study of dozens of assemblies done with Newbler 2.3 and this problem occurs:
- on gDNA from bacteria
- on gDNA from eukarya
- on cDNA (option -cdna) from plantae
But I all cases have some example cons.

Using the same raw datas we obtained different behaviour from newbler.
If we provide a sff file, contigs will be mainly composed by '*' what is not true if we basicly convert this file into fasta and assmble it with newbler. If doing so the asmmbly will look just fine.
Where could the behaviour difference could come from ?

Still investigate...

Last edited by nicolallias; 10-15-2010 at 12:02 AM.
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