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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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Is option --n-ceil for reads only or also reference? #456

Open AlineMuyle opened 6 months ago

AlineMuyle commented 6 months ago

Hi, I have a reference which can contain a relatively high number of Ns (to correct for reference mapping bias at heterozygous sites). I was wondering if option --n-ceil for the maximum number of ambiguous characters applies only to the read or also to the reference (i.e. to the alignment globally)? Thanks in advance for your help

ch4rr0 commented 6 months ago

Hello,

--n-ceil applies only to the read. You may want to try the --np which:

Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N. Default: 1.

I hope this helps.

AlineMuyle commented 6 months ago

Thank you for your answer. So if I understand there is no threshold on the number of Ns in the reference, as long as the associated penalty does not affect the mapping score too much? I will do some tests with --np 0. Thanks again and happy new year!