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Old 03-28-2014, 06:57 AM   #1
id0
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Default STAR multi-mapping

By default, STAR outFilterMultimapNmax parameter (read alignments will be output only if the read maps fewer than this value) is set to 10. Should that just be set to 1 if you are going to process the data with htseq-count, which discards multi-mapped reads? Is there a benefit to leaving it at 10?
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Old 03-28-2014, 07:41 AM   #2
alexdobin
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Default

Quote:
Originally Posted by id0 View Post
By default, STAR outFilterMultimapNmax parameter (read alignments will be output only if the read maps fewer than this value) is set to 10. Should that just be set to 1 if you are going to process the data with htseq-count, which discards multi-mapped reads? Is there a benefit to leaving it at 10?
Even if you keep multimappers in the SAM output, HTseq will not count them - it recognizes the unique mappers by NH:i:1 attribute.
Whether multimappers are useful depends on your downstream analysis. I find it useful to generate wiggle tracks separately for unique and multi-mappers, sometimes you can miss expression if you only look at unique mappers. Also, other quantification software (e.g. Cufflinks) can "rescue" multi-mappers. Typically multimappers do not occupy a lot of space, and - if needed - can be easily filtered by NH flag or the MAPQ field.
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