View Single Post
Old 07-03-2015, 02:36 AM   #1
wiki wiki
Location: Cambridge, England

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


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?
Homepage: Dan Bolser
MetaBase the database of biological databases.
dan is offline   Reply With Quote