<p>Is there a parameter in STAR for setting the minimum length of reads to be mapped?</p>

<p>In the &quot;Log.final.out&quot; file, there is a category, &quot;% of reads unmapped: too short,&quot; how do I change the &quot;too short&quot; variable?</p>

I was able to answer my own question:

The following parameters reduced my "Too short" percent from 10.8% to ~4%. Most of the reads went to multi-mapped or "other," but at least it worked.

    --seedSearchStartLmax 30  # increase overall mapping sensitivity
    --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0  --outFilterMatchNmin 50 # allow output of short alignments

There apparently isn't a minimum read length threshold for STAR.