Is there a parameter in STAR for setting the minimum length of reads to be mapped?
In the "Log.final.out" file, there is a category, "% of reads unmapped: too short," how do I change the "too short" variable?
Maybe this question can help you ? Do you know the length of those unmapped reads ?
That question is a decent start, but it doesn't specify what I'm trying to do... I'm comparing percent of reads mapped between STAR and GSNAP. GSNAP automatically throws out reads less that 17 bp. I was wondering if there is a parameter similar in STAR.
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.
STAR version 2.4.2a provides this option:
In this case, it requires a minimum 20 bp match.
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