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alexdobin / STAR

RNA-seq aligner
MIT License
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multi mapping parameters and centromere #2110

Open ptranvan opened 5 months ago

ptranvan commented 5 months ago

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, and outSAMmultNmax 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.

alexdobin commented 5 months ago

Hi Patrick, Yes, increasing these parameters is needed to capture multimappers.

ptranvan commented 5 months ago

Thanks @alexdobin for your quick response.

1) Do you have any recommended values?

2) Also, I am wondering how I can compare coverage between different samples. Do you know any normalization methods?

alexdobin commented 5 months ago

--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.