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--outFilterMultimapNmax and --outSAMmultNmax should be set to the maximum number of loci you want to map the reads.
--winAnchorMultimapNmax should twice as large.
However, if these values become too large (>~500), the mapping will be very slow.
Hi,
I am interested in looking at the mapping rate in the centromeres and was wondering which parameters I can tweak.
For TEs, I read that
winAnchorMultimapNmax
,outFilterMultimapNmax
, andoutSAMmultNmax
are commonly tweaked.What is your advice for repetitive regions such as centromeres? I am unsure about the parameters and the values I should set.
Thanks.
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