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?
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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