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5.6 years ago

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?

RNA-Seq STAR • 9.8k views
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Hi,

Maybe this question can help you ? Do you know the length of those unmapped reads ?

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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.

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5.6 years ago

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.

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STAR version 2.4.2a provides this option:

--outFilterMatchNmin 20


In this case, it requires a minimum 20 bp match.