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Old 07-03-2015, 02:36 AM   #1
dan
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Location: Cambridge, England

Join Date: Jul 2008
Posts: 266
Lightbulb FASTQ alignment metrics (RNA-Seq)?

Hello,

How do people judge the quality of a FASTQ (short read) alignment? In particular I'm interested in evaluating RNA-Seq alignments, typically (but not exclusively) from ILLUMINA instruments.

What comes to mind is:
* Fraction of reads mapped
* Fraction of reads mapped uniquely
* Fraction of 'good' pairs (right orientation, right distance)

and for RNA-Seq specifically
* Fraction of reads mapping within a gene

Anything based on read mapping quality?

What other metrics can we think of?
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