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Old 10-11-2017, 02:04 PM   #47
Location: boston

Join Date: Feb 2012
Posts: 30

Hi Brian,

I am wondering for BBsplit (with ambiguous2=split) if it is expected behavior that if I provide 2 references:

Ref 1 has 1 sequence that is a perfect match to PE sequencing reads
Ref 2 has many unique sequences that are at least 1 MM different from sequencing reads

For BBsplit to think the reads are ambiguously mapped? And for this to be the case for >90% of read pairs but not for every read pair?

Is there a way to force BBsplit to select Ref1 (perfect) over the options in Ref2?

I am trying to remove a nearly-identical putative contaminant sequence from my data...

(FYI I have ambiguous is set to best, and I've also tried setting both ambiguous and ambiguous2 to best, but the reads are almost all considered to be ambiguous in that scenario too)

Thx! Kate

Last edited by sk8bro; 10-11-2017 at 02:08 PM.
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