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Old 05-18-2017, 07:06 AM   #228
phylloxera
Junior Member
 
Location: Nebraska

Join Date: May 2017
Posts: 2
Default re: different results from command line and geneious plugin

Yes, the adapters files are different. Geneious says using All Truseq, Nextera, and PhiX adapters (152) sequences. The count in the resources folder of bbmap is 154 sequences. I don't know which 2 are lacking from geneious, presuming the shared set is 152. I could not find the adapters file geneious is calling... or the stats.txt file I asked it to produce. May need to call in Geneious support to help with this. Among the top stats.txt hits in the linux output are pcr dimer (16% of reads) and pcr primers (15% of reads). I wonder if these are lacking in geneious... Geneious is trimming more sequences by overlap 206,591 vs 157,344 and fewer sequences by ktrim 2,630,578 vs 2,657,654. Now... which one is best? The one trimming more?
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