STAR - multi-mapping reads cut off

Question

[is.birds]

Hi,

I've been using STAR (v 2.6.1b) to align RNA-seq and Poly-Ribo-seq reads to the human reference genome (hg38). The next steps in my pipeline use multi-mapping reads as part of a quality filter.

Here is an example excerpt from a STAR log file:

MULTI-MAPPING READS:
    Number of reads mapped to multiple loci |   11334616
         % of reads mapped to multiple loci |   17.56%
    Number of reads mapped to too many loci |   797072
         % of reads mapped to too many loci |   1.23%

I can't find any information about the threshold for "reads mapped to too many loci". Can anyone help with this? I'd just like to know what "too many" actually means.

Thanks!

Answer 1

[h.mon]

The default "too many" for STAR is above 10 mapping locations. This value is controlled by the parameter --outFilterMultimapNmax.