Difference between revisions of "HLab:Qualitymetrics"

Revision as of 15:10, 25 August 2014

ChIP-seq Guidelines from ENCODE (2012) article

FRIP: Fraction of Reads in Peaks, a value of greater than or equal to 0.01 is considered good.
NSC: Normalized Strand Coefficient, The normalized ratio between the fragment-length cross-correlation peak and the background cross-correlation. A value of greater than or equal to 1.05 is considered good.
RSC: Relative Strand Correlation, ratio between the fragment-length peak and the read-length peak. A value of greater than or equal to 0.8 is considered good.
Complexity: This is computed on a sampling of the reads if more than 10M, using Georgi's method. A value greater than or equal to 0.80 is considered good.
Duplication level: The duplication rate reported by FastQC. It is based on all reads even those that do not map.
Percent GC: The percent of nucleotides that are GC as reported by FastQC. It is based on all reads even those that do not map.

Standards, Guidelines and Best Practices for RNA-Seq V1.0 (June 2011)

FRIT: Fraction of Reads in Target, for Total script this is anywhere in the gene.
Percent rRNA: Percent of the alignments that overlap rRNA as downloaded from UCSC.
Number of expressed genes: Count of genes with RSEM TPM greater than 1. Should be similar between replicates.
Number of spike-ins: Count of reads mapping to spike-ins.

@@ Line 10: / Line 10: @@
 ;Complexity
 : This is computed on a sampling of the reads if more than 10M, using Georgi's method. A value greater than or equal to 0.80 is considered good.
+;Duplication level
+: The duplication rate reported by FastQC.  It is based on all reads even those that do not map.
+;Percent GC
+: The percent of nucleotides that are GC as reported by FastQC.  It is based on all reads even those that do not map.
 == RNA-seq ==